Habeeb
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habeebrahman.bsky.social
Habeeb
@habeebrahman.bsky.social
Postdoc at Marquette University. Interested in microbial interactions, biofilms and antimicrobials.
Reposted by Habeeb
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules. academic.oup.com/ismecommun/a...
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules
Abstract. Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most m
academic.oup.com
November 25, 2025 at 8:56 AM
Reposted by Habeeb
Excited to share our latest research in @natmicrobiol.nature.com . We uncover hundreds of inhibitory interactions between common chemical pollutants and human gut bacteria. A thread🧵 (1/10) #microbiomesky #microsky @kiranrpatil.bsky.social lab @mrc-tu.bsky.social www.nature.com/articles/s41...
Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro - Nature Microbiology
Screening of 1,076 compounds reveals 168 chemical pollutants with inhibitory effects on gut bacteria and genetic screens indicate commonality between pollutant and antibiotic resistance.
www.nature.com
November 26, 2025 at 10:30 AM
Reposted by Habeeb
Really happy to see the final version of this published in @isme-microbes.bsky.social. We show that production of and competition for biotin shapes S. aureus fitness in the context of nasal commensals doi.org/10.1093/isme...
Work lead by the amazing Kevser Bilici!
Competitive fitness of Staphylococcus aureus against nasal commensals depends on biotin biosynthesis and acquisition
Abstract. The human nasal microbiome can serve as a reservoir for pathogens. In particular, the opportunistic pathogen Staphylococcus aureus can be a membe
doi.org
November 24, 2025 at 5:54 PM
Reposted by Habeeb
Exciting post-doc opportunity in the group of Chris Quince (Earlham/Quadram) on novel ‘omics methods for the study of the human microbiome

jobs.quadram.ac.uk/Details.asp?...
Quadram Institute
jobs.quadram.ac.uk
November 21, 2025 at 12:26 PM
Reposted by Habeeb
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Reposted by Habeeb
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations

We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.

EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.

#WAAW2025 #ActOnAMR

www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Reposted by Habeeb
Apply now to attend the next EMBO Bacterial Networks meeting #EMBOBacNet

🗓️13-18 September 2026
📍Sant Feliu de Guixols, Spain

📝Program and registration info: meetings.embo.org/event/26-bac...

👩‍🔬Organised with co-chair @s-lab.bsky.social and ECR @coralietesseur.bsky.social

#MicroSky
November 20, 2025 at 10:16 AM
Reposted by Habeeb
Why does daptomycin resistance appear so fast in Enterococcus? We finally have a clue.

DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin https://www.biorxiv.org/content/10.1101/2025.11.16.688641v1
November 17, 2025 at 8:27 PM
Reposted by Habeeb
Bacteria have to adapt rapidly to changes in environment. Can they ‘remember’ those conditions? Another one for my “to read” pile! cc @microberamon.bsky.social @victoriachu.bsky.social @nickyuen.bsky.social @fratorelli.bsky.social #UTISky #MicroSky
November 18, 2025 at 9:13 AM
Reposted by Habeeb
#NewResearch

A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated C. difficile infection in mice.

#MicroSky 🦠💊

www.nature.com/articles/s41...
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - Nature Microbiology
A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated Clostridioides difficile infection in mice.
www.nature.com
November 18, 2025 at 2:07 PM
Reposted by Habeeb
Interesting paper

'Monoclonal antibody anti-PBP2a from Methicillin-resistant Staphylococcus aureus (MRSA) binds PBP5 from Enterococcus faecium and confers protection in a murine model'

pubmed.ncbi.nlm.nih.gov/41238026/
When cross-reaction is welcome: Monoclonal antibody anti-PBP2a from Methicillin-resistant Staphylococcus aureus (MRSA) binds PBP5 from Enterococcus faecium and confers protection in a murine model - PubMed
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) pose significant global concerns, particularly with the limited availability of new antibiotics. Therefore, alternative treatment approaches are needed. In this study, the potential cro …
pubmed.ncbi.nlm.nih.gov
November 17, 2025 at 11:22 AM
Reposted by Habeeb
Assembly, architecture and functional roles of microbial surface layers

Review article published in @natrevmicro.nature.com with @bupbuse.bsky.social, Andriko von Kügelgen and @vikramalva.bsky.social.

S-layers are everywhere!

www.nature.com/articles/s41...
Assembly, architecture and functional roles of microbial surface layers - Nature Reviews Microbiology
Surface layers (S-layers) are ubiquitous protein assemblies that coat prokaryotic cells, with their functional roles increasingly coming into focus. In this Review, Isbilir and colleagues discuss rece...
www.nature.com
November 13, 2025 at 8:14 PM
Reposted by Habeeb
Let me use this as an opportunity to talk about Jordi et al's very cool paper, now out in PNAS 🧪:

pmc.ncbi.nlm.nih.gov/articles/PMC...

You can read our news and views here: www.pnas.org/doi/10.1073/...
November 13, 2025 at 4:13 PM
Reposted by Habeeb
Kudos to our superstar grad student @sophiejwalton.bsky.social! One of the most interesting and surprising (at least to me) studies I have been involved in. Very curious to know what people think of it! @benjaminhgood.bsky.social
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:37 PM
Reposted by Habeeb
Low doses of tEDTA kill P. aeruginosa in models of chronic wound and CF lung #biofilm, but not in a model of endotracheal tube colonisation: preprint from a project led by @tosinorababa.bsky.social and implemented by a crack team of PhD students! #MicroSky www.biorxiv.org/content/10.1...
Low concentrations of tetrasodium EDTA cause significant killing of biofilm-associated P. aeruginosa in high validity models of chronic wound and CF lung infections but not in a model of endotracheal tube colonisation
Pseudomonas aeruginosa is a pathogen notorious for its antimicrobial resistance and is currently classified as a high-priority pathogen for which new drugs are needed. Tetrasodium EDTA (tEDTA) is one of the new antimicrobial compounds that have been shown to have good antibacterial and antibiofilm efficacy against P. aeruginosa. Due to the diversity and highly drug-tolerant nature of P. aeruginosa biofilms in different infection environments, it is important to carry out pre-clinical testing of new antibiofilm agents against this pathogen in media and models that accurately mimic diverse infection environments. In this study, we used different high validity media and biofilm models that mimic chronic wounds, endotracheal tubes, and cystic fibrosis lung infections to assess the efficacy of tEDTA against P. aeruginosa biofilms. We report that different infection environments influence the susceptibility of both planktonic and biofilm forms of P. aeruginosa to tEDTA. The highest tolerance to tEDTA was observed in the media and biofilm model that mimics the endotracheal tube environment. In conclusion, we show that although different infection environments influence the efficacy of tEDTA against P. aeruginosa biofilms, it has good potential for use as an alternative antimicrobial in treating P. aeruginosa-associated biofilm infections. ### Competing Interest Statement The authors have declared no competing interest.
www.biorxiv.org
November 10, 2025 at 10:21 AM
Reposted by Habeeb
Heroic work by @bluebirdsjunk.bsky.social in pulling this mammoth study together

'Staphylococcus haemolyticus Population Genomics Provides Insights into Pathogenicity and Commensalism'

www.biorxiv.org/content/10.1...
Staphylococcus haemolyticus Population Genomics Provides Insights into Pathogenicity and Commensalism
Staphylococcus haemolyticus is a common commensal bacterium but also an opportunistic pathogen, frequently implicated in bacteraemia and sepsis in preterm neonates and immunocompromised patients. Desp...
www.biorxiv.org
November 11, 2025 at 10:04 AM
Reposted by Habeeb
New paper: www.sciencedirect.com/science/arti...
Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.
mgrB inactivation confers enhanced pathogenicity and immune evasion over mcr-1 expression in colistin-resistant Klebsiella pneumoniae
Colistin is one of the last treatment options against human infections caused by multi-drug resistant Klebsiella pneumoniae. Colistin resistant K. pne…
www.sciencedirect.com
November 6, 2025 at 12:13 PM
Reposted by Habeeb
𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 𝘤𝘰𝘦𝘭𝘪𝘤𝘰𝘭𝘰𝘳 A3(2) produces a so far unknown antibiotic (because no one has looked closer, that is)
#MicroSky
🙏thx for pointing this out @microbingle.bsky.social
October 28, 2025 at 7:50 PM
Reposted by Habeeb
🎓 #PhDPosition !

🍽️ The impact of innovative food ingredients on the human gut microbiome and health with Dr Fred Warren @starchlab.bsky.social

📅Apply by 2 December

➡️ buff.ly/zaFaqGk
October 29, 2025 at 8:02 AM
Reposted by Habeeb
PhD position on Regulation and Evolution of Bacterial Multicellularity ( #Streptomyces ) within @spp2389.bsky.social supervised by Natalia Tschowri (Hannover 🇩🇪) and Danny Rozen (Leiden 🇳🇱) with research at both locations

deadline: October 31, 2025

www.uni-hannover.de/en/jobs/id/802
October 8, 2025 at 1:18 PM
Reposted by Habeeb
New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
September 25, 2025 at 2:31 PM
Reposted by Habeeb
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Faculty Professor Associate - Full-Time | Vaughn Cooper
We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...
www.linkedin.com
September 23, 2025 at 10:31 PM
Reposted by Habeeb
Rifampicin is more effective against biofilm infections because it targets biofilm-forming mutants that are highly resistant to other antibiotics @niaidnews.bsky.social
www.science.org/doi/10.1126/...
September 17, 2025 at 10:28 PM
Reposted by Habeeb
Genome evolution of Acinetobacter baylyi ADP1 during laboratory domestication: acquired mutations impact competence and metabolism

#ApplEnvironMicrobiol from Jeff Barrick

journals.asm.org/doi/10.1128/...
Genome evolution of Acinetobacter baylyi ADP1 during laboratory domestication: acquired mutations impact competence and metabolism | Applied and Environmental Microbiology
Acinetobacter baylyi ADP1 is a bacterial chassis of interest to microbiologists in academia and industry due to its extreme natural competence and wide metabolic range. Its ability to take up DNA from...
journals.asm.org
September 18, 2025 at 11:14 AM