Malte Rühlemann
@malte.ruehlemann.io
(he/his)
human microbiome science and genetics
first-gen
PI in CRC1182 (@crc1182.bsky.social)
PostDoc at IKMB / Poyet-Groussin Labs (@mmmicrobiomelab.bsky.social)
Kiel, Germany
human microbiome science and genetics
first-gen
PI in CRC1182 (@crc1182.bsky.social)
PostDoc at IKMB / Poyet-Groussin Labs (@mmmicrobiomelab.bsky.social)
Kiel, Germany
💡 Takeaway: In children, enterotypes aren’t innate—they’re ecological outcomes of postnatal microbial colonization and diet. Prevotella-rich states are possible, but take longer to emerge. 🧬🌱 7/n
📄 Link to paper: doi.org/10.1038/s415...
📄 Link to paper: doi.org/10.1038/s415...
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...
doi.org
April 7, 2025 at 8:03 AM
💡 Takeaway: In children, enterotypes aren’t innate—they’re ecological outcomes of postnatal microbial colonization and diet. Prevotella-rich states are possible, but take longer to emerge. 🧬🌱 7/n
📄 Link to paper: doi.org/10.1038/s415...
📄 Link to paper: doi.org/10.1038/s415...
🚸 Weaning as a switch: Mutation rates in gut microbes spiked after weaning, especially in genes for carb metabolism—a likely response to dietary transition. This may help explain enterotype restructuring. 🍞🧪 6/n
April 7, 2025 at 8:03 AM
🚸 Weaning as a switch: Mutation rates in gut microbes spiked after weaning, especially in genes for carb metabolism—a likely response to dietary transition. This may help explain enterotype restructuring. 🍞🧪 6/n
🧬 Strain-level perspective: The team reconstructed nearly 4,000 MAGs, tracking which strains persisted or were replaced. Bacteroides strains were more stable, while Prevotella appeared later and were less persistent. ⏳🧫 5/n
April 7, 2025 at 8:03 AM
🧬 Strain-level perspective: The team reconstructed nearly 4,000 MAGs, tracking which strains persisted or were replaced. Bacteroides strains were more stable, while Prevotella appeared later and were less persistent. ⏳🧫 5/n
🧠 Ecological insight: The Bacteroides–Prevotella divide mirrors adult enterotype structure. But in kids, these configurations are late-emerging, dynamic, and not fixed, challenging static interpretations of enterotypes. ⚖️📉 4/n
April 7, 2025 at 8:03 AM
🧠 Ecological insight: The Bacteroides–Prevotella divide mirrors adult enterotype structure. But in kids, these configurations are late-emerging, dynamic, and not fixed, challenging static interpretations of enterotypes. ⚖️📉 4/n
🔄 Prevotella dynamics: While less common, Prevotella-dominated states emerged in some children only after age 4. These were mutually exclusive with Bacteroides and often linked to specific dietary contexts. 🥕🦠 3/n
April 7, 2025 at 8:03 AM
🔄 Prevotella dynamics: While less common, Prevotella-dominated states emerged in some children only after age 4. These were mutually exclusive with Bacteroides and often linked to specific dietary contexts. 🥕🦠 3/n
📊 Enterotype emergence: Most infants begin with a low-Bacteroides profile. After weaning, many transition into adult-like enterotypes—primarily Bacteroides-dominated, but also some Prevotella-rich configurations. 🔁🥄 2/n
April 7, 2025 at 8:03 AM
📊 Enterotype emergence: Most infants begin with a low-Bacteroides profile. After weaning, many transition into adult-like enterotypes—primarily Bacteroides-dominated, but also some Prevotella-rich configurations. 🔁🥄 2/n
Yes, same! Great piece with some very quotable lines: "Science requires us to be open: we constantly need to follow the data, to branch out in new directions. […] Openness allows creative endeavors to evolve."
April 2, 2025 at 2:55 PM
Yes, same! Great piece with some very quotable lines: "Science requires us to be open: we constantly need to follow the data, to branch out in new directions. […] Openness allows creative endeavors to evolve."
🌍 Implications: This model shifts how we view human origins—from panmictic simplicity to structured complexity with implications for selection, ancestry, and interaction with archaic hominins. 🧬📜 6/n
📄 Link to paper: www.nature.com/articles/s41...
📄 Link to paper: www.nature.com/articles/s41...
A structured coalescent model reveals deep ancestral structure shared by all modern humans - Nature Genetics
The cobraa model extends the pairwise sequentially Markovian coalescent to identify structured population history by examination of the model transition matrix. Applied to human polymorphism data, cob...
www.nature.com
March 18, 2025 at 12:04 PM
🌍 Implications: This model shifts how we view human origins—from panmictic simplicity to structured complexity with implications for selection, ancestry, and interaction with archaic hominins. 🧬📜 6/n
📄 Link to paper: www.nature.com/articles/s41...
📄 Link to paper: www.nature.com/articles/s41...
🧠 Functional Impact: Regions enriched for minor (B) ancestry include genes tied to neuronal functions, while regions depleted in B ancestry involve immune responses, hinting at selective pressures post-admixture. 🧠🔬 5/n
March 18, 2025 at 12:04 PM
🧠 Functional Impact: Regions enriched for minor (B) ancestry include genes tied to neuronal functions, while regions depleted in B ancestry involve immune responses, hinting at selective pressures post-admixture. 🧠🔬 5/n
💡 Link to Archaic Humans: The majority (A) lineage shows closer genetic ties to Neanderthals and Denisovans, suggesting A was ancestral to archaic humans, while B’s contribution was more distant and selected against. 🧬🦴 4/n
March 18, 2025 at 12:04 PM
💡 Link to Archaic Humans: The majority (A) lineage shows closer genetic ties to Neanderthals and Denisovans, suggesting A was ancestral to archaic humans, while B’s contribution was more distant and selected against. 🧬🦴 4/n
🦠 Ancestral Structure: After splitting, population A experienced a bottleneck, while B remained larger. Selection appears to have acted against B’s genetic contribution in humans today, especially near coding regions. ⚔️🧬 3/n
March 18, 2025 at 12:04 PM
🦠 Ancestral Structure: After splitting, population A experienced a bottleneck, while B remained larger. Selection appears to have acted against B’s genetic contribution in humans today, especially near coding regions. ⚔️🧬 3/n
🔑 Key Idea: Rather than a single ancestral population, modern humans trace their lineage to deeply structured populations. Cobraa distinguishes these using coalescent patterns in genome sequences. 🧬📊 2/n
March 18, 2025 at 12:04 PM
🔑 Key Idea: Rather than a single ancestral population, modern humans trace their lineage to deeply structured populations. Cobraa distinguishes these using coalescent patterns in genome sequences. 🧬📊 2/n
Good point. They mention Dorea longicatena as another potential candidate to reduce C.diff infection due to its similar capacity for proline fermentation / Stickland fermentation.
March 7, 2025 at 2:15 PM
Good point. They mention Dorea longicatena as another potential candidate to reduce C.diff infection due to its similar capacity for proline fermentation / Stickland fermentation.
💡 Implications: This study moves beyond FMTs, showing how a rationally designed microbial therapy can replace donor stool with precisely defined consortia, improving safety and reproducibility. 🎯💊 6/n
📄 Link to paper: www.sciencedirect.com/science/arti...
📄 Link to paper: www.sciencedirect.com/science/arti...
A designed synthetic microbiota provides insight to community function in Clostridioides difficile resistance
Clostridioides difficile, a major cause of antibiotic-associated diarrhea, is suppressed by the gut microbiome, but the precise mechanisms are not ful…
www.sciencedirect.com
March 6, 2025 at 11:59 AM
💡 Implications: This study moves beyond FMTs, showing how a rationally designed microbial therapy can replace donor stool with precisely defined consortia, improving safety and reproducibility. 🎯💊 6/n
📄 Link to paper: www.sciencedirect.com/science/arti...
📄 Link to paper: www.sciencedirect.com/science/arti...
🐭 P. anaerobius Alone Protects: Mono-colonization with P. anaerobius provided protection equivalent to human FMT in a gnotobiotic mouse model, suggesting potential for a single-strain therapy. 🏥🦠 5/n
March 6, 2025 at 11:59 AM
🐭 P. anaerobius Alone Protects: Mono-colonization with P. anaerobius provided protection equivalent to human FMT in a gnotobiotic mouse model, suggesting potential for a single-strain therapy. 🏥🦠 5/n
🦠 Proline Fermentation is Key: Rather than bile acid metabolism, proline-fermenting bacteria, especially Peptostreptococcus anaerobius, were necessary and sufficient for suppressing C. difficile via nutrient competition. 🔄🥩 4/n
March 6, 2025 at 11:59 AM
🦠 Proline Fermentation is Key: Rather than bile acid metabolism, proline-fermenting bacteria, especially Peptostreptococcus anaerobius, were necessary and sufficient for suppressing C. difficile via nutrient competition. 🔄🥩 4/n
🤖 Machine Learning Design: The team analyzed 12 human microbiome studies, identifying microbes negatively associated with C. difficile. These predictive signatures guided the design of sFMT1. 📊🛠️ 3/n
March 6, 2025 at 11:59 AM
🤖 Machine Learning Design: The team analyzed 12 human microbiome studies, identifying microbes negatively associated with C. difficile. These predictive signatures guided the design of sFMT1. 📊🛠️ 3/n
🔑 Key Idea: Rather than relying on human donor FMTs, this study shows that a designed microbiome can provide targeted protection, identifying specific bacterial functions responsible for pathogen suppression. 🧬🦠 2/n
March 6, 2025 at 11:59 AM
🔑 Key Idea: Rather than relying on human donor FMTs, this study shows that a designed microbiome can provide targeted protection, identifying specific bacterial functions responsible for pathogen suppression. 🧬🦠 2/n