New PERSPECTIVE - A decade of advances in human gut microbiome-derived biotherapeutics
by Alena Pribyl, Phil Hugenholtz & Matthew Cooper
www.nature.com/articles/s41...
by Alena Pribyl, Phil Hugenholtz & Matthew Cooper
www.nature.com/articles/s41...
A decade of advances in human gut microbiome-derived biotherapeutics - Nature Microbiology
This Perspective reflects on advances made in the field of human gut microbiome-derived biotherapeutics, from faecal microbiota products to rationally designed second- and third-generation live biothe...
www.nature.com
January 8, 2025 at 12:05 PM
New PERSPECTIVE - A decade of advances in human gut microbiome-derived biotherapeutics
by Alena Pribyl, Phil Hugenholtz & Matthew Cooper
www.nature.com/articles/s41...
by Alena Pribyl, Phil Hugenholtz & Matthew Cooper
www.nature.com/articles/s41...
Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples - @uchichemistry.bsky.social bit.ly/3TYj96P
Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples - Nature Biotechnology
Colorectal cancer is discriminated by measuring cell-free RNA methylation in plasma.
bit.ly
July 8, 2025 at 3:52 PM
Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples - @uchichemistry.bsky.social bit.ly/3TYj96P
Happy to share the latest from the lab! A microbiome-generated metabolite affects male-male aggression and social dominance in mice via the main olfactory system. Gut-Nose-Behavior.
www.cell.com/current-biol...
www.cell.com/current-biol...
A microbiome-derived olfactory signal regulates inter-male aggression and social dominance in mice
Cichy et al. show that trimethylamine (TMA), a gut microbiome-derived metabolite,
activates the receptor TAAR5 in the main olfactory system to regulate aggression and
social dominance in male mice. Th...
www.cell.com
March 30, 2026 at 6:32 PM
Happy to share the latest from the lab! A microbiome-generated metabolite affects male-male aggression and social dominance in mice via the main olfactory system. Gut-Nose-Behavior.
www.cell.com/current-biol...
www.cell.com/current-biol...
#GastroEdPick A decade of advances in human gut microbiome-derived biotherapeutics
@naturemicrobiol.bsky.social www.nature.com/articles/s41...
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@naturemicrobiol.bsky.social www.nature.com/articles/s41...
🦠
A decade of advances in human gut microbiome-derived biotherapeutics - Nature Microbiology
This Perspective reflects on advances made in the field of human gut microbiome-derived biotherapeutics, from faecal microbiota products to rationally designed second- and third-generation live biothe...
www.nature.com
January 10, 2025 at 9:27 AM
#GastroEdPick A decade of advances in human gut microbiome-derived biotherapeutics
@naturemicrobiol.bsky.social www.nature.com/articles/s41...
🦠
@naturemicrobiol.bsky.social www.nature.com/articles/s41...
🦠
If you have ever wondered what might happen to short chain fatty acids made by the microbiome. Here is a large class of metabolites and how they link to biology. www.cell.com/cell/fulltex...
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids
Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library
containing hundreds of N-acyl lipids, including conjugates with short-chain fatty
acids. This resource enabled the...
www.cell.com
June 12, 2025 at 5:56 PM
If you have ever wondered what might happen to short chain fatty acids made by the microbiome. Here is a large class of metabolites and how they link to biology. www.cell.com/cell/fulltex...
Nature research paper: Commensal-derived acetylcholine enhances mucosal immune education
go.nature.com/3RJ1r9L
go.nature.com/3RJ1r9L
Commensal-derived acetylcholine enhances mucosal immune education - Nature
A diet–microbiome–host axis strengthens mucosal immune defences and reinforces host–microbiota mutualism.
go.nature.com
June 8, 2026 at 8:30 AM
Nature research paper: Commensal-derived acetylcholine enhances mucosal immune education
go.nature.com/3RJ1r9L
go.nature.com/3RJ1r9L
How Staph. lugdunensis controls production of its anti-S. aureus effector lugdunin
@cmfi.bsky.social @dzif.bsky.social
The human microbiome-derived antimicrobial lugdunin self-regulates its biosynthesis by a feed-forward mechanism
journals.asm.org/doi/10.1128/...
@cmfi.bsky.social @dzif.bsky.social
The human microbiome-derived antimicrobial lugdunin self-regulates its biosynthesis by a feed-forward mechanism
journals.asm.org/doi/10.1128/...
March 19, 2025 at 7:53 AM
How Staph. lugdunensis controls production of its anti-S. aureus effector lugdunin
@cmfi.bsky.social @dzif.bsky.social
The human microbiome-derived antimicrobial lugdunin self-regulates its biosynthesis by a feed-forward mechanism
journals.asm.org/doi/10.1128/...
@cmfi.bsky.social @dzif.bsky.social
The human microbiome-derived antimicrobial lugdunin self-regulates its biosynthesis by a feed-forward mechanism
journals.asm.org/doi/10.1128/...
Looks interesting 👀: Distinguishing diet- and microbe-derived metabolites in the human gut microbiomejournal.biomedcentral.com/articles/10....
Distinguishing diet- and microbe-derived metabolites in the human gut - Microbiome
Background Human gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbio...
microbiomejournal.biomedcentral.com
October 18, 2025 at 7:07 PM
Looks interesting 👀: Distinguishing diet- and microbe-derived metabolites in the human gut microbiomejournal.biomedcentral.com/articles/10....
CONGRATS to team @effectomics.bsky.social and @steidele.bsky.social . Transcriptional Response of Magnaporthe oryzae Towards Barley-Microbiome Derived Bacteria | Molecular Plant-Microbe Interactions® apsjournals.apsnet.org/doi/10.1094/...
Transcriptional Response of Magnaporthe oryzae Towards Barley-Microbiome Derived Bacteria | Molecular Plant-Microbe Interactions®
The composition of the plant microbiome is shaped not only by the host plant and abiotic environmental factors, but also by inter-microbial cooperation and competition. Plant pathogens, therefore must...
apsjournals.apsnet.org
December 20, 2025 at 2:19 PM
CONGRATS to team @effectomics.bsky.social and @steidele.bsky.social . Transcriptional Response of Magnaporthe oryzae Towards Barley-Microbiome Derived Bacteria | Molecular Plant-Microbe Interactions® apsjournals.apsnet.org/doi/10.1094/...
Another report today on revving up cancer immunotherapy response via gut microbiome manipulation (derived from patients, tested in experiential model)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses - Nature Microbiology
Hexa-acylated lipopolysaccharides from the gut microbiota are associated with efficacy in patients with cancer receiving anti-PD-1 and stimulate host immune activation for enhanced anti-tumour immunit...
www.nature.com
February 10, 2025 at 3:30 PM
Another report today on revving up cancer immunotherapy response via gut microbiome manipulation (derived from patients, tested in experiential model)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Let's go to mars with moss!
Moss-derived microbiome improves crop growth in lunar and Martian soil simulants
www.sciencedirect.com/science/arti...
Moss-derived microbiome improves crop growth in lunar and Martian soil simulants
www.sciencedirect.com/science/arti...
Moss-derived microbiome improves crop growth in lunar and Martian soil simulants
This study evaluates the potential of a moss–microbe complex, composed of Hypnum plumaeforme and its associated microorganisms, as a bio-based biofert…
www.sciencedirect.com
August 19, 2025 at 9:25 AM
Let's go to mars with moss!
Moss-derived microbiome improves crop growth in lunar and Martian soil simulants
www.sciencedirect.com/science/arti...
Moss-derived microbiome improves crop growth in lunar and Martian soil simulants
www.sciencedirect.com/science/arti...
Data duplication reported in influential Nature paper on gut microbiome-brain axis
pubpeer.com/publications...
pubpeer.com/publications...
PubPeer - A gut-derived metabolite alters brain activity and anxiety b...
There are comments on PubPeer for publication: A gut-derived metabolite alters brain activity and anxiety behaviour in mice (2022)
pubpeer.com
February 8, 2026 at 9:44 AM
Data duplication reported in influential Nature paper on gut microbiome-brain axis
pubpeer.com/publications...
pubpeer.com/publications...
Its stories like this that makes me incredibly excited!
A gut immune–epithelial circuit regulating tolerance to food:
Goblet cell protein RELMβ disrupts tolerance by depleting microbiome-derived indoles needed for protective Tregs.
#microbiome #immunity #ImmunoSky
www.nature.com/articles/s41...
A gut immune–epithelial circuit regulating tolerance to food:
Goblet cell protein RELMβ disrupts tolerance by depleting microbiome-derived indoles needed for protective Tregs.
#microbiome #immunity #ImmunoSky
www.nature.com/articles/s41...
January 27, 2025 at 10:13 PM
Its stories like this that makes me incredibly excited!
A gut immune–epithelial circuit regulating tolerance to food:
Goblet cell protein RELMβ disrupts tolerance by depleting microbiome-derived indoles needed for protective Tregs.
#microbiome #immunity #ImmunoSky
www.nature.com/articles/s41...
A gut immune–epithelial circuit regulating tolerance to food:
Goblet cell protein RELMβ disrupts tolerance by depleting microbiome-derived indoles needed for protective Tregs.
#microbiome #immunity #ImmunoSky
www.nature.com/articles/s41...
Congrats to our research unit member Annika Cichy @cichy1985.bsky.social !🎉 Check out her new publication: www.cell.com/current-biol...
A microbiome-derived chemical cue shapes mammalian social behavior via olfaction
A microbiome-derived chemical cue shapes mammalian social behavior via olfaction
A microbiome-derived olfactory signal regulates inter-male aggression and social dominance in mice
Cichy et al. show that trimethylamine (TMA), a gut microbiome-derived metabolite,
activates the receptor TAAR5 in the main olfactory system to regulate aggression and
social dominance in male mice. Th...
www.cell.com
March 30, 2026 at 7:10 PM
Congrats to our research unit member Annika Cichy @cichy1985.bsky.social !🎉 Check out her new publication: www.cell.com/current-biol...
A microbiome-derived chemical cue shapes mammalian social behavior via olfaction
A microbiome-derived chemical cue shapes mammalian social behavior via olfaction
Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42...
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
Metagenomic estimation of dietary intake from human stool - Nature Metabolism
Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.
www.nature.com
February 18, 2025 at 11:02 AM
Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42...
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
We investigated and identified several skin-derived bacteria that antagonize common pathogenic species: www.nature.com/articles/s41...
A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo
A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo
Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome - Nature Communications
Authors present the EPithelial Isolate Collection (EPIC), a large skin microbiome culture collection, uncovering new species, widespread antifungal activity, and hidden biosynthetic diversity, reveali...
www.nature.com
August 3, 2026 at 3:41 AM
We investigated and identified several skin-derived bacteria that antagonize common pathogenic species: www.nature.com/articles/s41...
A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo
A cool highlight was that bacteria from feet, where fungi are particularly diverse, tended to be more broadly antifungal than those from other body sites! #microevo
In our latest preprint, led by Master's student Gechlang Tang, we put forth a modest proposal: why not just use host-derived reads as a normalization factor for estimating absolute bacterial biomass in stool metagenomes? 🦠💩📈
@isbscience.org
www.biorxiv.org/content/10.1...
@isbscience.org
www.biorxiv.org/content/10.1...
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.
Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such ...
www.biorxiv.org
January 8, 2025 at 4:56 PM
In our latest preprint, led by Master's student Gechlang Tang, we put forth a modest proposal: why not just use host-derived reads as a normalization factor for estimating absolute bacterial biomass in stool metagenomes? 🦠💩📈
@isbscience.org
www.biorxiv.org/content/10.1...
@isbscience.org
www.biorxiv.org/content/10.1...
💥 Big news! We’ve secured €750K for the RUMBA project through the Synergistic Projects call.
We’ll decode microbiota-derived molecules to boost immunotherapy in lung cancer. The microbiome takes the stage! 🦠🫁 🧪
#microbiome #immunotherapy #lungcancer
We’ll decode microbiota-derived molecules to boost immunotherapy in lung cancer. The microbiome takes the stage! 🦠🫁 🧪
#microbiome #immunotherapy #lungcancer
June 24, 2025 at 10:01 PM
💥 Big news! We’ve secured €750K for the RUMBA project through the Synergistic Projects call.
We’ll decode microbiota-derived molecules to boost immunotherapy in lung cancer. The microbiome takes the stage! 🦠🫁 🧪
#microbiome #immunotherapy #lungcancer
We’ll decode microbiota-derived molecules to boost immunotherapy in lung cancer. The microbiome takes the stage! 🦠🫁 🧪
#microbiome #immunotherapy #lungcancer
Super excited to share that my PhD research paper is finally out!
@newphyt.bsky.social
doi.org/10.1111/nph....
@parkergroup.bsky.social
@newphyt.bsky.social
doi.org/10.1111/nph....
@parkergroup.bsky.social
Cooperation between a root fungal endophyte and host‐derived coumarin scopoletin mediates Arabidopsis iron nutrition
Iron acquisition is a critical challenge for plants, especially in iron-deficient soils. Recent research underscores the importance of root-exuded coumarins in modulating the root microbiome communi.....
doi.org
August 21, 2025 at 10:55 AM
Super excited to share that my PhD research paper is finally out!
@newphyt.bsky.social
doi.org/10.1111/nph....
@parkergroup.bsky.social
@newphyt.bsky.social
doi.org/10.1111/nph....
@parkergroup.bsky.social
Super interesting study investigating a commensal bacteria that looks to contain metabolic products that impact the development of fat. Study highlights a microbiome /immune cell and metabolism network 🧵🧪
A commensal-derived sugar protects against obesity by regulating immunometabolism
Tan et al. identify a human commensal bacterium, Clostridium immunis—and its bioactive
phosphocholine-modified exopolysaccharide (EPS)—that reduces visceral adiposity and
weight gain in mice. By decre...
www.cell.com
September 27, 2026 at 7:35 AM
Super interesting study investigating a commensal bacteria that looks to contain metabolic products that impact the development of fat. Study highlights a microbiome /immune cell and metabolism network 🧵🧪
Nature research paper: The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour
https://go.nature.com/4519XFK
https://go.nature.com/4519XFK
The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour - Nature
A distinct population of CD4 T cells resides in specific regions of the steady-state brain, and these T cells are programmed in the periphery by the microbiome to coordinate adaptive behaviour.
go.nature.com
June 2, 2025 at 6:18 PM
Nature research paper: The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour
https://go.nature.com/4519XFK
https://go.nature.com/4519XFK
ICYMI: New online! Is precision microbiome medicine just around the corner?
Is precision microbiome medicine just around the corner?
Nature Reviews Gastroenterology & Hepatology, Published online: 04 February 2025; doi:10.1038/s41575-025-01040-4A study in Nature Medicine developed a new clinical test based on a gut metagenome-derived multispecies biomarker panel for the diagnosis of…
www.nature.com
February 5, 2025 at 3:42 PM
ICYMI: New online! Is precision microbiome medicine just around the corner?
🚨by Hiroshi Yasuda @Yash25571056 about gut microbiome & Covid:
"SIM01 (a gut microbiota-derived synbiotic formula) hastened antibody formation against SARS-CoV-2, reduced nasopharyngeal viral load, reduced pro-inflammatory immune markers, & restored..."
Short 🧵:
threadreaderapp.com/thread/19601...
"SIM01 (a gut microbiota-derived synbiotic formula) hastened antibody formation against SARS-CoV-2, reduced nasopharyngeal viral load, reduced pro-inflammatory immune markers, & restored..."
Short 🧵:
threadreaderapp.com/thread/19601...
August 27, 2025 at 1:54 PM
🚨by Hiroshi Yasuda @Yash25571056 about gut microbiome & Covid:
"SIM01 (a gut microbiota-derived synbiotic formula) hastened antibody formation against SARS-CoV-2, reduced nasopharyngeal viral load, reduced pro-inflammatory immune markers, & restored..."
Short 🧵:
threadreaderapp.com/thread/19601...
"SIM01 (a gut microbiota-derived synbiotic formula) hastened antibody formation against SARS-CoV-2, reduced nasopharyngeal viral load, reduced pro-inflammatory immune markers, & restored..."
Short 🧵:
threadreaderapp.com/thread/19601...