Manuel Kleiner
@manuelkleiner.bsky.social
Associate Professor, Microbiomes and Complex Microbial Communities, North Carolina State University Microbiology, Host-Microbe Interactions, Microbial Ecophysiology, Proteomics and Metaproteomics https://kleinerlab.cals.ncsu.edu/
Which is your favourite database?
DSMZ Digital Diversity@dsmzd3.bsky.social · yesterdayℹ️DSMZ Digital Diversity is a consortium of ten integrated biological databases 🖥️🧬 that are provided by @leibniz-dsmz.bsky.social🧫 and are of high relevance to life science research🔬, with four of them having been named #ELIXIR and #GlobalBiodata core resources. Which of our databases do you use?
TriMic: a Triticum aestivum microbial culture collection and synthetic community for dissecting wheat-microbe interactions bioRxiv from Clara Tang et al from @manuelkleiner.bsky.social #INTERACT project funded by @novo-nordisk.bsky.social www.biorxiv.org/content/10.6...
TriMic: a Triticum aestivum microbial culture collection and synthetic community for dissecting wheat-microbe interactions
Understanding the molecular mechanisms underlying plant–microbe interactions is essential for developing innovative microbe-based agrotechnologies. However, deciphering these mechanisms within the com...
biorxiv.org
New: TriMic collection of wheat root microbes and a synthetic community to study plant health. Details: www.biorxiv.org/content/10.6... #Microbiome #SustainableAg 📷 pixabay/Alexas_Fotos
We just released a curated, fully genome sequence isolate collection from wheat roots (TriMic). It is publicly available as individual strains and cost effective bundles from the amazing @leibniz-dsmz.bsky.social bioresource center www.biorxiv.org/content/10.6... We will expand it in the future
TriMic: a Triticum aestivum microbial culture collection and synthetic community for dissecting wheat-microbe interactions
Understanding the molecular mechanisms underlying plant-microbe interactions is essential for developing innovative microbe-based agrotechnologies. However, deciphering these mechanisms within the com...
biorxiv.org
Our new paper is out in #mSystems! Quantify total and active bacterial cells from environmental samples with MATRIX! @asm.org @cnrs.fr @universitelyon.bsky.social journals.asm.org/doi/10.1128/...
MATRIX: rapid quantification of total and active microbial cells with single-cell phenotypes for environmental microbiomes | mSystems
Microbiome studies commonly rely on relative abundance data, which cannot distinguish whether compositional shifts reflect true population growth, declines in total community size, or both. Without ex...
journals.asm.org
The type and amount of bacterial DNA carried by virus-like particles in the gut microbiome is simply mind-boggling. Amazing work by PhD candidate Jessie Maier in my group and collaborators @duerkoplab.bsky.social and Ben Callahan www.biorxiv.org/content/10.6...
Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome
Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of...
biorxiv.org
We developed a new method for the ultra-purification of virus-like particles that will allow to run high throughput VLP purifications for #virome studies, while achieving the same purity or better than CsCl density gradient ultracentrifugation. www.biorxiv.org/content/10.6...
High throughput chromatographic ultra-purification of virus-like particles for downstream viromics
Virus-like particles (VLPs) are an abundant component of microbiomes with critical ecological roles such as population control through viral predation and horizontal gene transfer. Studying the collec...
biorxiv.org
🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0
A new blog post on a microbiome/cancer study that earns a second thought rather than just a nod or a shrug: merenlab.org/blog/sacchar... And LET THE RECORD SHOW that this post COMPLETELY addresses the incorrect claim that Meren only complains about microbiome studies.
A probiotic yeast, colorectal cancer, and the gut microbiome
A rare correlative microbiome study careful enough to think with, and an arrow or two I would redraw.
merenlab.org
Even after all these years and thousands and thousands of single cells, there continue to be surprises in this field. proteomicsnews.blogspot.com/2026/05/brid...
Bridging simplicity and depth in single cell proteomics.- some neat observations!
I do like it when a new group gets on the the single cell proteomics train and starts optimizing/reoptimizing things. Despite the 300 revie...
proteomicsnews.blogspot.com
Why would you cite a reference if you haven’t read the fricking paper (b/c in your case it’s in another language)? I sometimes have an organic chemistry prof stop by, asking me to translate a section in an old paper (when ochem was done mostly by old german dudes). That’s scholarship! Also, fuck AI!
Dr. Holly Walters@manigarm.bsky.social · 3mo agoI'm sorry, what? In writing my first monograph, I spent six weeks trying to track down a citation in TWO languages I didn't know. And good thing too, because the citation was wrong. That's scholarship. That's research. You know, the thing we're trained to do?!?
In the latest issue of Food & Function: Assessing the diversity and functional profile of the “microbial proteome” in fermented foods. #OpenAccess from Ayesha Awan, Manuel Kleiner et al @manuelkleiner.bsky.social Read now: pubs.rsc.org/en/content/a...
Assessing the diversity and functional profile of the “microbial proteome” in fermented foods
Fermented foods are staples in diets worldwide and are known for their health benefits. Microorganisms are the key to fermented food production as they convert raw substrates into digestible, nutritio...
pubs.rsc.org
Thank you to @sciam.bsky.social for letting me dig into the protein enhancement fad. 1. If you are an elite athlete, OR elderly/frail, maybe you do need extra protein. 2. That's not you. You're not an elite athlete. 3. If it is you: consider yogurt. www.scientificamerican.com/article/prot...
Are protein-boosted foods and drinks actually more healthy?
Extra protein can be found in everything now, from potato chips to Pop-Tarts. Does this benefit the average eater?
scientificamerican.com
COMMBAT: a web platform for exploring expression control of biosynthetic gene clusters @narjournal.bsky.social from @sebarigali.bsky.social With @gillesvanwezel.bsky.social @marnixmedema.bsky.social academic.oup.com/nar/advance-...
COMMBAT: a web platform for exploring expression control of biosynthetic gene clusters
Abstract. Bacterial genomes contain thousands of biosynthetic gene clusters (BGCs) responsible for the production of structurally diverse natural products
academic.oup.com
See a brief review summarizing the use of synthetic microbial communities (SynComs) for revealing the ecology of specialized metabolites [my holiday break writing exercise] portlandpress.com/essaysbioche... #MicrobiomeEcology at Institute of Biology Leiden (IBL)
J. Craig Venter, Scientist Who Decoded the Human Genome, Dies at 79 A risk-taking outsider, he brought speed, competition and controversy to one of science’s biggest races. #GiftLink Nicholas Wade writes @NYtimes.com www.nytimes.com/2026/04/30/s...
J. Craig Venter, Scientist Who Decoded the Human Genome, Dies at 79
nytimes.com
Come work with me at the Department of Soil Biology in Hohenheim, Postdoc position for three years. I am looking for someone who will support my current line of research and help establish novel methods of molecular soil ecology in the lab. Thanks for sharing. www.uni-hohenheim.de/stellenangeb...
Stellenangebote: Universität Hohenheim
Aktuelle Stellenangebote der Universität Hohenheim.
uni-hohenheim.de
8 more days left to apply for this 3-year postdoc position. Please repost! The position offers a lot of freedom to test new ideas about how archaea and bacteria communicate & sense the extracellular environment.
Amelia Rotaru@ameliarotaru.bsky.social · 5mo agoPlease help spread the word about this 3-year postdoc position in my team. If your expertise & interest lie in studying how organisms from different domains of life (Bacteria and Archaea) communicate, come join us this summer in cozy Odense, Denmark. Job post: www.nature.com/naturecareer...
We evaluated quantification methods for #metaproteomics and found that area under the curve quantification (AUC) outperforms spectral counting. Importantly, using match between runs for AUC quantification results in lots of false detections and should not be used www.biorxiv.org/content/10.6...
biorxiv.org
We have developed an automated tool for transductomics called TrIdent to detect DNA carried in virus-like particles in microbiomes. Quite amazing to see how much DNA carriage is happening in gut microbiomes. www.biorxiv.org/content/10.6...
biorxiv.org
I thought it was quite mind boggling to see that around 10% of the protein in a standard yeast based bread is actually yeast protein! Here our #metaproteomics analysis of microbial protein in fermented foods pubs.rsc.org/en/Content/A... Congratulations to first authors Laura Winkler and Ayesha Awan
Assessing the diversity and functional profile of the “microbial proteome” in fermented foods
Fermented foods are staples in diets worldwide and are known for their health benefits. Microorganisms are the key to fermented food production as they convert raw substrates into digestible, nutritio...
pubs.rsc.org
We just released a curated, fully genome sequence isolate collection from Maize roots (ZeaMiC). It is publicly available as individual strains and cost effective bundles from the amazing @leibniz-dsmz.bsky.social culture collection www.biorxiv.org/content/10.6... We hope to expand it in the future
biorxiv.org
This is becoming a bit of a problem for Nature titles... retractionwatch.com/2026/03/06/l...
Librarian finds ‘preposterous number’ of fake references in paper from Springer Nature journal
Gunnar Ridderström/Pexels As a hospital librarian, Jessica Waite is typically successful at tracking down elusive articles for clinicians at Royal Hallamshire Hospital in England. So when a colleag…
retractionwatch.com
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others academic.oup.com/femsre/artic... 🧵👇
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
academic.oup.com
🆕 Vacancy! We’re looking for a motivated Research Scientist to join the laboratory of Dr @lizsayavedra.bsky.social in our Food, Microbiome and Health programme. 💷 £37,500 to £45,350 🗓️ Apply by 22 March 2026 ➡️ buff.ly/VwXSgWQ
If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you jobs.ncsu.edu/postings/226...
Postdoctoral Research Scholar
The Callahan Lab at NC State University (https://callahanlab.cvm.ncsu.edu/team/) is seeking a postdoctoral scholar to study the transfer of DNA between bacteria (horizontal gene transfer;HGT) by virus...
jobs.ncsu.edu
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction. www.biorxiv.org/content/10.6...
Check out our new preprint using 30 SynComs covering a phylogenetic diversity gradient, we uncover many interesting strain and community features involved in seed to seedling bacterial transmission 🧫🌱 @emersys-irhs.bsky.social in the SUCSEED project @inrae-dpt-spe.bsky.social
Gontran Arnault@garnault.bsky.social · 6mo ago🌱 New preprint with @microbialmarie.bsky.social www.biorxiv.org/content/10.6... Bacterial Strain Identity and Community Composition Drive the Seed-to-Seedling Microbiota Assembly We explore which strain traits and community features explain successful bacterial transmission from seed to seedling.⬇️
