Raymond Kiu
@raymondkiu.bsky.social
Research Fellow with Hall Lab @halllab.bsky.social at the Institute of Microbiology & Infection @imibirmingham.bsky.social & Quadram Institute | Gut microbiome | Metagenomics | Microbial genomics | AMR 🧬🦠🇬🇧
🔗 https://linktr.ee/raymondkiu
🔗 https://linktr.ee/raymondkiu
Reposted by Raymond Kiu
Have research, results, or ideas to share with the microbial ecology community? Don’t miss your chance to present it at #MMEG2025 - abstract submissions close 2 November!
📨 Submit your abstract: appliedmicrobiology.org/ems-event-ca...
📨 Submit your abstract: appliedmicrobiology.org/ems-event-ca...
October 13, 2025 at 4:49 PM
Have research, results, or ideas to share with the microbial ecology community? Don’t miss your chance to present it at #MMEG2025 - abstract submissions close 2 November!
📨 Submit your abstract: appliedmicrobiology.org/ems-event-ca...
📨 Submit your abstract: appliedmicrobiology.org/ems-event-ca...
Reposted by Raymond Kiu
It’s been a bit over 2 months since the main results of my PhD work on reconstructing carbohydrate utilization pathways in human bifidobacteria were finally published; so I guess it’s a good time to update the previous thread (1/7) www.nature.com/articles/s41...
September 30, 2025 at 9:01 AM
It’s been a bit over 2 months since the main results of my PhD work on reconstructing carbohydrate utilization pathways in human bifidobacteria were finally published; so I guess it’s a good time to update the previous thread (1/7) www.nature.com/articles/s41...
Reposted by Raymond Kiu
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Wonderful plenary lecture by Prof Dena Lyras to kick off Clostpath 2025 in Paris! @pasteuredu.bsky.social @monashuniversity.bsky.social #clostpath14
September 1, 2025 at 5:21 PM
Wonderful plenary lecture by Prof Dena Lyras to kick off Clostpath 2025 in Paris! @pasteuredu.bsky.social @monashuniversity.bsky.social #clostpath14
Reposted by Raymond Kiu
Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com!
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
August 17, 2025 at 11:54 PM
Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com!
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨
Huge team effort!
www.nature.com/articles/s41...
Reposted by Raymond Kiu
💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥
I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com
@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social
www.cell.com/cell-systems...
🧵...
I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com
@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social
www.cell.com/cell-systems...
🧵...
Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut
Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized
Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key
metabolic strategies ex...
www.cell.com
August 6, 2025 at 4:51 PM
💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥
I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com
@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social
www.cell.com/cell-systems...
🧵...
I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com
@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social
www.cell.com/cell-systems...
🧵...
Reposted by Raymond Kiu
Very cool. Here, authors did pairwise co-culturing (mGAM/anaerobiosis) of 97 gut microbial species (113 strains) to infer ecological interactions (n=3233). Most negative were between distant taxa & positive were more among low-abundance taxa.
🔗 microbiomejournal.biomedcentral.com/articles/10....
🔗 microbiomejournal.biomedcentral.com/articles/10....
Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria - Microbiome
Background Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, the...
microbiomejournal.biomedcentral.com
July 16, 2025 at 3:05 PM
Very cool. Here, authors did pairwise co-culturing (mGAM/anaerobiosis) of 97 gut microbial species (113 strains) to infer ecological interactions (n=3233). Most negative were between distant taxa & positive were more among low-abundance taxa.
🔗 microbiomejournal.biomedcentral.com/articles/10....
🔗 microbiomejournal.biomedcentral.com/articles/10....
Reposted by Raymond Kiu
Around 25% of U.S. infants lack detectable Bifidobacterium, regardless of birth or feeding method. This deficit could have implications for immune health and the trajectory of noncommunicable diseases, according to a study published in Communications Biology. go.nature.com/4lgA1ls 🧪
July 14, 2025 at 1:54 AM
Around 25% of U.S. infants lack detectable Bifidobacterium, regardless of birth or feeding method. This deficit could have implications for immune health and the trajectory of noncommunicable diseases, according to a study published in Communications Biology. go.nature.com/4lgA1ls 🧪
Reposted by Raymond Kiu
🦠 ClostPath 2025 is coming to Paris! 🇫🇷
Join us Sept 1-4, 2025 at Institut Pasteur for the 14th International Conference on Molecular Biology & Pathogenesis of Clostridia.
📝 Register now: www.clostpath2025.conferences-pasteur.org/home
Join us Sept 1-4, 2025 at Institut Pasteur for the 14th International Conference on Molecular Biology & Pathogenesis of Clostridia.
📝 Register now: www.clostpath2025.conferences-pasteur.org/home
July 11, 2025 at 11:09 AM
🦠 ClostPath 2025 is coming to Paris! 🇫🇷
Join us Sept 1-4, 2025 at Institut Pasteur for the 14th International Conference on Molecular Biology & Pathogenesis of Clostridia.
📝 Register now: www.clostpath2025.conferences-pasteur.org/home
Join us Sept 1-4, 2025 at Institut Pasteur for the 14th International Conference on Molecular Biology & Pathogenesis of Clostridia.
📝 Register now: www.clostpath2025.conferences-pasteur.org/home
Reposted by Raymond Kiu
Day 4 of IMI Summer school started with Feeding the Future and green bread 🍞 with UoB's Dr Helen Onyeaka, GI infections with Dr Ella Rodwell and Exploring the World of Gut Bacteria with the fabulous @halllab.bsky.social 🦠🦠🦠
July 3, 2025 at 12:02 PM
Day 4 of IMI Summer school started with Feeding the Future and green bread 🍞 with UoB's Dr Helen Onyeaka, GI infections with Dr Ella Rodwell and Exploring the World of Gut Bacteria with the fabulous @halllab.bsky.social 🦠🦠🦠
Reposted by Raymond Kiu
Peter Wildy Prize Lecture and Interview with Prof. Lindsay Hall from Annual Conference 2025 is now available on YouTube. Watch the full interview and lecture: 'Guardians of the Gut Bringing Microbiome Science to Life through Public Engagement' microb.io/40s1zvB #Microbio25
July 3, 2025 at 11:03 AM
Peter Wildy Prize Lecture and Interview with Prof. Lindsay Hall from Annual Conference 2025 is now available on YouTube. Watch the full interview and lecture: 'Guardians of the Gut Bringing Microbiome Science to Life through Public Engagement' microb.io/40s1zvB #Microbio25
Reposted by Raymond Kiu
Half way through the IMI Summer school 2025 starts with a fantastic Q&A panel with our own UoB students and Postdocs and @wvschaik.bsky.social giving a great talk on AMR & Phages 🦠🦠
July 2, 2025 at 12:30 PM
Half way through the IMI Summer school 2025 starts with a fantastic Q&A panel with our own UoB students and Postdocs and @wvschaik.bsky.social giving a great talk on AMR & Phages 🦠🦠
Reposted by Raymond Kiu
How does your diet impact the microbiome? Let's find out...🦠🦠
July 2, 2025 at 2:05 PM
How does your diet impact the microbiome? Let's find out...🦠🦠
Reposted by Raymond Kiu
Culture club! Do probiotic yoghurt drinks really contain live bacteria? Let's find out at IMI Summer school 2025 🦠🦠
July 1, 2025 at 1:20 PM
Culture club! Do probiotic yoghurt drinks really contain live bacteria? Let's find out at IMI Summer school 2025 🦠🦠
Reposted by Raymond Kiu
🌍 #WorldMicrobiomeDay 2025
At @halllab.bsky.social we’re uncovering how microbes - right from day one - help shape the gut, strengthen immunity, and protect against infection.
We're exploring how, when, and which microbes colonise - in order to develop interventions for a healthier start to life.
At @halllab.bsky.social we’re uncovering how microbes - right from day one - help shape the gut, strengthen immunity, and protect against infection.
We're exploring how, when, and which microbes colonise - in order to develop interventions for a healthier start to life.
June 27, 2025 at 9:44 AM
🌍 #WorldMicrobiomeDay 2025
At @halllab.bsky.social we’re uncovering how microbes - right from day one - help shape the gut, strengthen immunity, and protect against infection.
We're exploring how, when, and which microbes colonise - in order to develop interventions for a healthier start to life.
At @halllab.bsky.social we’re uncovering how microbes - right from day one - help shape the gut, strengthen immunity, and protect against infection.
We're exploring how, when, and which microbes colonise - in order to develop interventions for a healthier start to life.
Reposted by Raymond Kiu
Newly published study by Prof Lindsay Hall @halllab.bsky.social and Prof Willem van Schaik @wvschaik.bsky.social finding that antibiotic resistant Staphylococcus haemolyticus bacteria are common in premature babies
www.birmingham.ac.uk/news/2025/wi...
www.birmingham.ac.uk/news/2025/wi...
June 30, 2025 at 2:51 PM
Newly published study by Prof Lindsay Hall @halllab.bsky.social and Prof Willem van Schaik @wvschaik.bsky.social finding that antibiotic resistant Staphylococcus haemolyticus bacteria are common in premature babies
www.birmingham.ac.uk/news/2025/wi...
www.birmingham.ac.uk/news/2025/wi...
Reposted by Raymond Kiu
#NatMicroPicks
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Gut microbiome evolution from infancy to 8 years of age - Nature Medicine
In a unique cohort of twins followed from birth to 8 years of age, shotgun sequencing of stool samples reveals that the transmission, persistence and evolutionary adaptation of bacterial strains are s...
www.nature.com
June 26, 2025 at 3:32 PM
#NatMicroPicks
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Reposted by Raymond Kiu
Amazing to see this now published! Congrats to @lisalamberte.bsky.social and @wvschaik.bsky.social - on leading this important #microbiome study on #AMR and Staphylococcus haemolyticus in the preterm gut 👇
I am delighted that our manuscript 'Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut' is now published.
www.tandfonline.com/doi/full/10....
Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social
www.tandfonline.com/doi/full/10....
Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social
Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut
Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemo...
www.tandfonline.com
June 23, 2025 at 10:34 AM
Amazing to see this now published! Congrats to @lisalamberte.bsky.social and @wvschaik.bsky.social - on leading this important #microbiome study on #AMR and Staphylococcus haemolyticus in the preterm gut 👇
Reposted by Raymond Kiu
I am delighted that our manuscript 'Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut' is now published.
www.tandfonline.com/doi/full/10....
Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social
www.tandfonline.com/doi/full/10....
Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social
Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut
Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemo...
www.tandfonline.com
June 23, 2025 at 10:13 AM
I am delighted that our manuscript 'Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut' is now published.
www.tandfonline.com/doi/full/10....
Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social
www.tandfonline.com/doi/full/10....
Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social
Reposted by Raymond Kiu
An exciting new Doctoral Training Programme in Microbial Genomics for Health Protection, in collaboration with the UK Health Security Agency @ukhsa.bsky.social, has just launched, funded by @nihr.bsky.social there are 9 PhD projects available (UK students only) www.birmingham.ac.uk/research/cen...
PhD Microbial Genomics for Health Protection, Biosciences - University of Birmingham
PhD in Microbial Genomics, exciting new Doctoral Training Programme in Microbial Genomics for Health Protection in collaboration with the UK Health Security Agency (UKHSA) launches
www.birmingham.ac.uk
May 23, 2025 at 8:34 AM
An exciting new Doctoral Training Programme in Microbial Genomics for Health Protection, in collaboration with the UK Health Security Agency @ukhsa.bsky.social, has just launched, funded by @nihr.bsky.social there are 9 PhD projects available (UK students only) www.birmingham.ac.uk/research/cen...
Reposted by Raymond Kiu
(1/6) 🌟 Excited to share our new paper!
Advancing microbiome safety assessments: opportunities, challenges & recommendations 🧫🦠
This work came out of an academic–industry workshop hosted by @microbiologysociety.org in early 2024.
🔗 www.microbiologyresearch.org/content/jour...
Advancing microbiome safety assessments: opportunities, challenges & recommendations 🧫🦠
This work came out of an academic–industry workshop hosted by @microbiologysociety.org in early 2024.
🔗 www.microbiologyresearch.org/content/jour...
Assessing the safety of microbiome perturbations
Everyday actions such as eating, tooth brushing or applying cosmetics inherently modulate our microbiome. Advances in sequencing technologies now facilitate detailed microbial profiling, driving inten...
www.microbiologyresearch.org
May 27, 2025 at 4:52 PM
(1/6) 🌟 Excited to share our new paper!
Advancing microbiome safety assessments: opportunities, challenges & recommendations 🧫🦠
This work came out of an academic–industry workshop hosted by @microbiologysociety.org in early 2024.
🔗 www.microbiologyresearch.org/content/jour...
Advancing microbiome safety assessments: opportunities, challenges & recommendations 🧫🦠
This work came out of an academic–industry workshop hosted by @microbiologysociety.org in early 2024.
🔗 www.microbiologyresearch.org/content/jour...
Reposted by Raymond Kiu
New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
(1/6)
www.biorxiv.org/content/10.1...
(1/6)
Autocycler: long-read consensus assembly for bacterial genomes
Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...
www.biorxiv.org
May 21, 2025 at 3:29 AM
New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
(1/6)
www.biorxiv.org/content/10.1...
(1/6)
Reposted by Raymond Kiu
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
May 1, 2025 at 6:41 PM
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
Reposted by Raymond Kiu
What happens to microbial genomic evolution in highly stable, closed ecosystems? In this preprint, authors look at 111 MAGs from a Romanian cave isolated from external influences for 5.5My(!) and see more pseudogenisation of core genes & limited HGT. Unsurprising?
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
April 11, 2025 at 5:51 AM
What happens to microbial genomic evolution in highly stable, closed ecosystems? In this preprint, authors look at 111 MAGs from a Romanian cave isolated from external influences for 5.5My(!) and see more pseudogenisation of core genes & limited HGT. Unsurprising?
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
Reposted by Raymond Kiu
Excited to finally share results from my first post-doc @halllab.bsky.social 🫡
E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation.
www.biorxiv.org/content/10.1...
E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation.
www.biorxiv.org/content/10.1...
www.biorxiv.org
April 9, 2025 at 3:12 PM
Excited to finally share results from my first post-doc @halllab.bsky.social 🫡
E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation.
www.biorxiv.org/content/10.1...
E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation.
www.biorxiv.org/content/10.1...