Maryse Berkhout

Mucin-dependent transcriptional dynamics of Akkermansia muciniphila in co-culture with human colonic organoids Abstract. Akkermansia muciniphila, a mucin-degrading gut bacterium, contributes to intestinal homeostasis and metabolic disorders, yet its transcriptional

doi.org/10.1093/bbb/...

The role of Akkermansia muciniphila sulfatases in colonic mucin utilisation Akkermansia muciniphila, an obligate mucin degrader, is a major member of the human colonic microbiota and has been associated positive health outcomes. Mucins are complex glycoproteins that contain h...

www.biorxiv.org/content/10.1...

Emerging probiotics: future therapeutics for human gut health Fibre-degrading gut anaerobes including important butyrate producers, lactate producers and utilizers, have been proposed here as next-generation probiotic

doi.org/10.1093/fems...

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts Bifidobacterium are beneficial members of the microbiota across animal hosts. Kujawska et al. demonstrate that bifidobacteria have likely co-evolved more closely with mammals, particularly primates, a...

www.cell.com/cell-host-mi...

#microsky #microbiome

#microsky #microbiomesky

Cell surface polysaccharides in the gut microbiota: occurrence, structure and role The gastrointestinal (GI) tract is colonized by trillions of microorganisms living in a symbiotic relationship with the host. Commensal bacteria in the gut engage in cross-talks with epithelial and...

www.tandfonline.com/doi/full/10....

#microsky #microbiome #glycotime

#Editorial

In this month's editorial, we talk about microbial foods. Bacteria and fungi can augment the flavour, composition and sustainability of foods, but more research is needed to push microbial foods — and consumer palates — to new heights.

#MicroSky 🦠

www.nature.com/articles/s41...

Niche-specific metabolic phenotypes can be used to identify antimicrobial targets in pathogens The emergence of resistance to traditional antimicrobials increases the need to develop innovative approaches to understanding pathogen function. This study uses a computational data-driven approach t...

journals.plos.org/plosbiology/...

#microsky

Ecological design of high-performance synthetic microbial communities: from theoretical foundations to functional optimization Abstract. The complexity of natural microbial communities poses significant challenges for predictive manipulation, driving the emergence of Synthetic Micr

Ecological design of high-performance synthetic microbial communities: from theoretical foundations to functional optimization

#SynCom

in #ISMEComms

academic.oup.com/ismecommun/a...

Milk and mucin glycans orchestrate a synthetic infant gut microbiota structure Dietary and gut glycans drive the composition of an in vitro synthetic community of infant gut microbes.

🍼 The full paper is published in @femsjournals.bsky.social Microbiology Ecology👇

#microsky

doi.org/10.1093/fems...

Interactions between a mother’s milk and baby's microbes To explore the interactions between a baby's gut microbes and mother's milk, a study applies a synthetic community of glycan degraders and cross-feeders.

💡 Curious how we applied a synthetic community to study interactions between baby gut microbes and a lot of different sugars?

📖 I wrote a blog for the #FEMSmicroBlog to explain!

🦠 #microsky #microbiomesky #glycotime

fems-microbiology.org/femsmicroblo...

About the interactions between sugars from mother’s milk and the baby’s microbes To explore the interactions between different sugars and the gut microbes in an infant, a new study applies a synthetic community consisting of glycan degraders and cross-feeders.

Milk sugars from the mother play crucial roles in the development of a baby's gut microbiome. 🍼

To explore the interactions between sugars and the gut microbes in an infant, a study applies a community of glycan degraders and cross-feeders. #FEMSmicroBlog #FascinatingMicrobes

A model of early-life interactions between the gut microbiome and adaptive immunity provides insights into the ontogeny of immune tolerance The developing immune system must learn which microbes to tolerate and which to resist, but how this process unfolds is unclear. This study develops a mechanistic mathematical model of early-life gut ...

New paper from Burcu - working towards describing 'immune education' journals.plos.org/plosbiology/...

Milk-derived casein glycomacropeptide improves colonic mucus function under Western-style diet feeding in a sialylation-dependent manner The colonic mucus layer is the primary interface between the host and the gut microbiota. It serves both as an ecological niche for bacteria and a bar…

Summer strike #2: Our collaboration work with Arla Foods Ingredients has just been published in Food Research International:

www.sciencedirect.com/science/arti...

#microsky #gastrosky #microbiomesky #guthealth

Applying ecological principles to microbiome engineering - Nature Microbiology This Perspective discusses the application of ecological principles of macro-ecosystems to microbiome engineering. The authors propose research priorities necessary to facilitate the application of th...

#Perspective

In this perspective, the authors propose research priorities necessary to facilitate the application of these ecological principles to improve microbiome functionality.

#MicroSky #MicrobiomeSky 🦠

www.nature.com/articles/s41...

Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision qPCR is used to measure soil microorganisms but can be affected by inhibitors, change in mastermix, and platform. This study measured precision and accurac

Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision

#FEMS Mcirobiol Ecol by @aoifeduff.bsky.social et al

academic.oup.com/femsec/artic...

Controlled colonization of the human gut with a genetically engineered microbial therapeutic Precision microbiome programming for therapeutic applications is limited by challenges in achieving reproducible colonic colonization. Previously, we created an exclusive niche that we used to engraft...

#microsky #microbiomesky

Controlled colonization of the human gut with a genetically engineered microbial therapeutic | Science www.science.org/doi/10.1126/...

Found: a human gut microbe that makes cancer therapy more effective in mice Cancer therapies called checkpoint inhibitor drugs, which ratchet up the immune system, work better when this bacterium is around.

Nice! A bacterium that is poorly described in literature can boost the function of check point therapy inhibitors in mice- shows the potential of microbiome that we have only just started to tap into -summary here 🧪 #MicroSky #ImmunoSky 🧵

However, when mucin was present, A. muciniphila thrived happily. 😎

GOS/FOS, which are often added as a prebiotic to infant formula, induced a similar microbial composition as HMOs.🍼

Although the microbial composition differed between all glycans, mucin was the main driver of dissimilarities.↔️

Even though the microbes in our synthetic community have similar glycan-degrading enzymes, their ability to grow in a community differs per glycan. ✂️

For example, Akkermansia muciniphila can grow on HMOs in monoculture, but was unable to compete with more specialist HMO degraders in the community.🔍

Milk and mucin glycans orchestrate a synthetic infant gut microbiota structure Dietary and gut glycans drive the composition of an in vitro synthetic community of infant gut microbes.

Another publication in @femsjournals.bsky.social @femsmicro.org 🔬

How do glycans shape the infant gut microbiota? 👶

With a novel in vitro synthetic community we studied the interplay between microbes and HMOs, mucin glycans and GOS/FOS.🍼🤱🦠

#microsky #glycotime

doi.org/10.1093/fems...

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria - Nature Microbiology A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

New RESOURCE!

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria

@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co

#microbiomesky #microsky

www.nature.com/articles/s41...

Thank you! We will definitely keep that in mind for future studies!

Growing different mono- and cocultures and the synthetic community on porcine gastric mucin led to distinct metabolite production profiles.

Butyrate was only produced in the synthetic community by cross-feeding bacteria.

👩‍🔬

We also tested mucin O-glycan degradation by these bacteria in cocultures and as part of a larger synthetic community, revealing interesting patterns.

The synthetic community was most efficient in degrading all present O- and N-glycans. Teamwork! 🦠🦠🦠

All three mucin glycan degraders released sialic acid🔸from porcine gastric mucin O-glycans, and R. torques had a preference for fucosylated structures🔺.

B. thetaiotaomicron preferred mucin O-glycans with core 2🟦🟡.

Distinct in vitro utilization and degradation of porcine gastric mucin glycans by human intestinal bacteria The degradation and utilization of mucin glycans depend on microbial composition and the interactions between the present bacteria.

Just published in @femsjournals.bsky.social🦠:

Akkermansia muciniphila, Ruminococcus torques and Bacteroides thetaiotaomicron differ in their preferences for degradation of porcine gastric mucin O- and N-glycans.

#microsky #microbiomesky #glycotime @mib-wur.bsky.social

doi.org/10.1093/fems...

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...

#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...

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

Happy #WorldMicrobiomeDay! 🦠

If you are a starter in this field, as I was until recently, here are some highly recommended articles from @natmicrobiol.nature.com that may help you understand, plan, and even improve your microbiome studies - A starter pack you might say! 😊🧵

#MicrobiomeSky #MicroSky