Mozammel Hoque
@mozammel.bsky.social
Playing with Unseen as Postdoctoral Research Associate Diane lab @AIMI_UTS exploiting molecular interaction of pathogenic bacteria and their predators.
https://scholar.google.com/citations?user=LN2GUkQAAAAJ&hl=en
https://scholar.google.com/citations?user=LN2GUkQAAAAJ&hl=en
Reposted by Mozammel Hoque
📢 New preprint is out on bioRxiv 📢:
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
November 27, 2025 at 8:44 PM
📢 New preprint is out on bioRxiv 📢:
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
By analysing microbial signatures from urine and catheters, we built a machine-learning tool that can distinguish harmful UTI-causing bacteria from harmless ones. This could help clinicians make better decisions about treatment and catheter changes, and importantly, avoid unnecessary antibiotics.
Thrilled to share our most challenging project yet! Our 3 years of longitudinal research, study on AI-based prediction of urinary tract infections (UTIs) in people with spinal cord injury is now published in Microbiome journal.
Here’s the link to the paper 👇 link.springer.com/article/10.1...
Here’s the link to the paper 👇 link.springer.com/article/10.1...
Prediction of symptomatic and asymptomatic bacteriuria in spinal cord injury patients using machine learning - Microbiome
Background Individuals with spinal cord injuries (SCI) frequently rely on urinary catheters to drain urine from the bladder, making them susceptible to asymptomatic and symptomatic catheter-associated...
link.springer.com
November 27, 2025 at 9:46 PM
By analysing microbial signatures from urine and catheters, we built a machine-learning tool that can distinguish harmful UTI-causing bacteria from harmless ones. This could help clinicians make better decisions about treatment and catheter changes, and importantly, avoid unnecessary antibiotics.
Thrilled to share our most challenging project yet! Our 3 years of longitudinal research, study on AI-based prediction of urinary tract infections (UTIs) in people with spinal cord injury is now published in Microbiome journal.
Here’s the link to the paper 👇 link.springer.com/article/10.1...
Here’s the link to the paper 👇 link.springer.com/article/10.1...
Prediction of symptomatic and asymptomatic bacteriuria in spinal cord injury patients using machine learning - Microbiome
Background Individuals with spinal cord injuries (SCI) frequently rely on urinary catheters to drain urine from the bladder, making them susceptible to asymptomatic and symptomatic catheter-associated...
link.springer.com
November 27, 2025 at 9:45 PM
Thrilled to share our most challenging project yet! Our 3 years of longitudinal research, study on AI-based prediction of urinary tract infections (UTIs) in people with spinal cord injury is now published in Microbiome journal.
Here’s the link to the paper 👇 link.springer.com/article/10.1...
Here’s the link to the paper 👇 link.springer.com/article/10.1...
November 27, 2025 at 8:36 PM
All artifact? 😬 www.pnas.org/doi/10.1073/...
Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS
Dihydrodichlorofluorescein derivatives have been employed as reporters of intracellular
reactive oxygen species (ROS) in innumerable studies. Their...
www.pnas.org
November 19, 2025 at 6:14 AM
All artifact? 😬 www.pnas.org/doi/10.1073/...
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome url: academic.oup.com/ismecommun/a...
Validate User
academic.oup.com
November 18, 2025 at 6:55 AM
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome url: academic.oup.com/ismecommun/a...
Reposted by Mozammel Hoque
🚨 Top microbiology jobs. The FEMS opportunities board has new PhD, Postdocs , & Junior Research Group roles in Methane Flux, AI in Health, Marine Symbiosis, & Evolution.
Apply here buff.ly/9r6E3Er or sign up for the monthly newsletter FEMS buff.ly/EQc3WTm .
Apply here buff.ly/9r6E3Er or sign up for the monthly newsletter FEMS buff.ly/EQc3WTm .
November 12, 2025 at 9:00 AM
🚨 Top microbiology jobs. The FEMS opportunities board has new PhD, Postdocs , & Junior Research Group roles in Methane Flux, AI in Health, Marine Symbiosis, & Evolution.
Apply here buff.ly/9r6E3Er or sign up for the monthly newsletter FEMS buff.ly/EQc3WTm .
Apply here buff.ly/9r6E3Er or sign up for the monthly newsletter FEMS buff.ly/EQc3WTm .
Reposted by Mozammel Hoque
Claude scientific skills 🧬🖥️🧪
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
November 12, 2025 at 10:14 AM
Claude scientific skills 🧬🖥️🧪
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
Reposted by Mozammel Hoque
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Mozammel Hoque
www.nature.com/articles/d41...
"Researchers welcome the initiative…" - no I fucking don't! This idea is dumber than a sack of hammers.
Basing any judgement on author position is crass - it captures very little of use and has no universal meaning.
"Researchers welcome the initiative…" - no I fucking don't! This idea is dumber than a sack of hammers.
Basing any judgement on author position is crass - it captures very little of use and has no universal meaning.
Google Scholar-based tool gives extra credit to first and last authors
Researchers welcome the initiative, but say it doesn’t go far enough to capture the nuance of researcher productivity and impact.
www.nature.com
October 27, 2025 at 3:57 PM
www.nature.com/articles/d41...
"Researchers welcome the initiative…" - no I fucking don't! This idea is dumber than a sack of hammers.
Basing any judgement on author position is crass - it captures very little of use and has no universal meaning.
"Researchers welcome the initiative…" - no I fucking don't! This idea is dumber than a sack of hammers.
Basing any judgement on author position is crass - it captures very little of use and has no universal meaning.
Reposted by Mozammel Hoque
A comprehensive review on microbial degradation of polyethylene plastics: ecotoxicity, deterioration process, recurrent intermediates and key enzymes involved link.springer.com/article/10.1... #jcampubs
A comprehensive review on microbial degradation of polyethylene plastics: ecotoxicity, deterioration process, recurrent intermediates and key enzymes involved - Archives of Microbiology
Plastic contamination is a universal threat that affects the flora and fauna in the environment. This review focuses on biodegradation of polyethylene (PE). PE is a widely used plastic in food packagi...
link.springer.com
October 27, 2025 at 6:18 AM
A comprehensive review on microbial degradation of polyethylene plastics: ecotoxicity, deterioration process, recurrent intermediates and key enzymes involved link.springer.com/article/10.1... #jcampubs
Check out our work on biofilm degrading enzyme. 👉Crude preparation of a phage-encoded biofilm-dispersing factor expressed in E. coli and its potential application in bacteriological analysis of environmental water samples | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...
Crude preparation of a phage-encoded biofilm-dispersing factor expressed in E. coli and its potential application in bacteriological analysis of environmental water samples | Applied and Environmental...
In their aquatic reservoirs, bacteria often exist as biofilms and are difficult to
accurately detect by culturing water samples. Such biofilms have been implicated in
waterborne transmission of pathog...
journals.asm.org
October 21, 2025 at 8:33 PM
Check out our work on biofilm degrading enzyme. 👉Crude preparation of a phage-encoded biofilm-dispersing factor expressed in E. coli and its potential application in bacteriological analysis of environmental water samples | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...
Reposted by Mozammel Hoque
Check out my PhD student Fiona Facey’s first first-author paper on finding microbes that can degrade multiple types of plastics in the Galleria mellonella gut microbiome
👇
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
👇
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Characterising the Multiple‐Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome
A novel strain of Bacillus subtilis has been isolated from plastic-fed Galleria mellonella larvae, which shows evidence of degradation of both LDPE and PU plastics. Genes potentially associated with ....
enviromicro-journals.onlinelibrary.wiley.com
October 21, 2025 at 5:09 AM
Check out my PhD student Fiona Facey’s first first-author paper on finding microbes that can degrade multiple types of plastics in the Galleria mellonella gut microbiome
👇
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
👇
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Mozammel Hoque
Glad to share a collaboration with Yicen Lin's group at Kunming University of Science and Technology published in ISME Journal
Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms
academic.oup.com/ismej/advanc...
#MicrobiomeEcology at #LeidenBiology
Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms
academic.oup.com/ismej/advanc...
#MicrobiomeEcology at #LeidenBiology
October 9, 2025 at 6:54 AM
Glad to share a collaboration with Yicen Lin's group at Kunming University of Science and Technology published in ISME Journal
Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms
academic.oup.com/ismej/advanc...
#MicrobiomeEcology at #LeidenBiology
Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms
academic.oup.com/ismej/advanc...
#MicrobiomeEcology at #LeidenBiology
Reposted by Mozammel Hoque
Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
August 15, 2025 at 1:54 PM
Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
Reposted by Mozammel Hoque
Cool PNAS paper by @jordivangestel.bsky.social and colleagues
Contributed by Carol Gross
[reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social]
Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation
www.pnas.org/doi/10.1073/...
Contributed by Carol Gross
[reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social]
Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation
www.pnas.org/doi/10.1073/...
September 25, 2025 at 6:29 PM
Cool PNAS paper by @jordivangestel.bsky.social and colleagues
Contributed by Carol Gross
[reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social]
Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation
www.pnas.org/doi/10.1073/...
Contributed by Carol Gross
[reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social]
Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation
www.pnas.org/doi/10.1073/...
Reposted by Mozammel Hoque
Delighted to announce that The International Meeting on the Biology of Vibrios will be back next year!
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Vibrio2026: The International Meeting on the Biology of Vibrios
Fourwaves - Vibrio2026: The International Meeting on the Biology of Vibrios
event.fourwaves.com
September 18, 2025 at 6:24 PM
Delighted to announce that The International Meeting on the Biology of Vibrios will be back next year!
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!
event.fourwaves.com/vibrio2026/p...
Reposted by Mozammel Hoque
Our second paper with @tcostalab.bsky.social and GoogleDeepMind
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
By solving a previously unsolved biological question, the AI co-scientist predicted
a complex mechanism of gene transfer and generated hypotheses that opened new research
directions, illustrating AI's...
www.cell.com
September 9, 2025 at 5:23 PM
Our second paper with @tcostalab.bsky.social and GoogleDeepMind
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
Reposted by Mozammel Hoque
Lots of heterogeneity in capsule production in Klebsiella and Acinetobacter. Given the pleiotropic impact of capsules, this provides opportunities for multiple types of phenotypical heterogeneity. Check @julielebris.bsky.social thread on our recent publication.
Delighted to share our recently published work!
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇
Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio
The polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. It is also an important virulence factor and a major ...
journals.asm.org
September 7, 2025 at 5:17 PM
Lots of heterogeneity in capsule production in Klebsiella and Acinetobacter. Given the pleiotropic impact of capsules, this provides opportunities for multiple types of phenotypical heterogeneity. Check @julielebris.bsky.social thread on our recent publication.
It’s was a great experience being part of the awesome organising team. 🥳
Until next year, @mozztacular.bsky.social, Asad, @royalfizzbin.bsky.social, Mozammel, @wytamma.bsky.social , Bec, and @rhyshparry.bsky.social out!
#MicroSeq2025
#MicroSeq2025
September 4, 2025 at 7:42 AM
It’s was a great experience being part of the awesome organising team. 🥳
Reposted by Mozammel Hoque
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 1, 2025 at 5:49 PM
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Reposted by Mozammel Hoque
Vibrio cholerae motility is associated with inter-animal transmission www.nature.com/articles/s41... 🦠
Vibrio cholerae motility is associated with inter-animal transmission - Nature Communications
Determinants of Vibrio cholerae transmission are incompletely understood. Here, the authors use an infant mouse model to show that events in the intestine govern inter-animal transmission and that bac...
www.nature.com
August 30, 2025 at 6:00 PM
Vibrio cholerae motility is associated with inter-animal transmission www.nature.com/articles/s41... 🦠
Reposted by Mozammel Hoque
My google skills are failing... Back in 2011, NCBI (started to?) close the SRA. The SRA is still with us. Anyone know of any articles from around then about how they saw the light? For those that this is news to...
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Closure of the NCBI SRA and implications for the long-term future of genomics data storage - Genome Biology
genomebiology.biomedcentral.com
August 30, 2025 at 10:06 PM
My google skills are failing... Back in 2011, NCBI (started to?) close the SRA. The SRA is still with us. Anyone know of any articles from around then about how they saw the light? For those that this is news to...
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Mozammel Hoque
Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...
The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance
The 2024 WHO BPPL is a key tool for prioritising research and development investments
and informing global public health policies to combat AMR. Gram-negative bacteria
and rifampicin-resistant M tuber...
www.thelancet.com
August 27, 2025 at 4:13 PM
Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...
Reposted by Mozammel Hoque
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Mathematical modelling for biologists - Modelling concepts in biological research
Mathematical modelling for biologists - Modelling concepts in biological research
www.ebi.ac.uk
August 15, 2025 at 10:39 AM
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples