W. Florian Fricke

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...

Looks interesting 👀: Distinguishing diet- and microbe-derived metabolites in the human gut microbiomejournal.biomedcentral.com/articles/10....

"both air sharing and physical contact enabled bidirectional transmission: U.S. mucus-degrading taxa (e.g., Akkermansia) was transferred into Thai microbiomes, while Thai-derived, potentially health-promoting bacteria colonized U.S. microbiomes." doi.org/10.1080/1949...

We're hiring a #postdoc with knowledge of the #microbiome, #microbiology, #bioinformatics, #computationalbiology to understand the role of the vaginal microbiome in women's health. #Baltimore #womenshealth

Learn more: bit.ly/CAMRIpostdoc

In #Microbiome:

🦠Exploring how the microbiome influences fertility & preconception health

🚨Offering a systems-level lens through which to understand & improve reproductive health by linking diet, immunity, metabolism & hormonal signaling

Read more👉 doi.org/p7cw

Cool paper: doi.org/10.1016/j.ce...
"different fermentation products [profiles] released [vary a lot more depending on] microbiome composition [than] daily production of bacterial biomass + release of fermentation products" "diet not microbiota [is] dominant factor for fermentation product harvest"

Congratulations to 1st author ‪@ninasusannschmidt.bsky.social‬ and other group members + thanks to collaborators Profs. Herbert Schmidt @unihohenheim.bsky.social‬ and Christian Sina ‪@uniluebeck.bsky.social‬ and the entire INDICATE team (6/x)

Our findings suggest new opportunities for personalized, non-invasive risk assessments, e.g. by screening patients with predisposing cardiac conditions + increased infective endocarditis risks for prophylactic antibiotic treatment before they undergo invasive dental procedures (5/x)

Humans from two independent cohorts could be reproducibly stratified based on dominant uGI bacterial clusters, with a Prevotella7-dominated ‘salivatype’ being maintained in the duodenum and associated with reduced burdens of GI (Fusobacterium) and non-GI (HACEK) opportunistic pathogens and TNF (4/x)

The murine uGI microbiota contained more typical intestinal bacteria, which were transcriptionally inactive in the esophagus and active in the duodenum, possibly due to coprophagy and horizontal microbiome exchange between mice (3/x)

We used a DNA+RNA-based methodology to study the upper gastrointestinal of mice and humans, while carefully assessing contamination, providing a blueprint for other, low-microbiome biomass microbiome studies (2/x)

Contamination-controlled upper gastrointestinal microbiota profiling reveals salivary-duodenal community types linked to opportunistic pathogen carriage and inflammation The upper gastrointestinal (uGI) microbiota has been implicated in infectious, metabolic, and immunological conditions, yet remains poorly characterized due to invasive sampling and low microbial b...

Can we predict small intestinal microbiota traits from saliva? Read our new paper “Contamination-controlled upper gastrointestinal microbiota profiling reveals salivary-duodenal community types linked to opportunistic pathogen carriage and inflammation”, doi.org/10.1080/1949...

Moving from genome-scale to community-scale metabolic models for the human gut microbiome - Nature Microbiology In this Perspective, Deiner, Gibbons and colleagues describe the current strengths and limitations of microbial community-scale metabolic models in microbiome research.

Microbial community-scale metabolic models (MCMMs) map gut microbiome composition & dietary context to functional outputs, at scale.

Here, we describe these emerging tools & their utility to both basic & translational microbiome research. @natmicrobiol.nature.com

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

A blueprint for contemporary studies of microbiomes - Microbiome This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...

New editorial at Microbiome 🦠 !
Co-authored by the Senior Editors, it aims to highlight current challenges in the field of environmental and host-associated microbiome research and provides a blueprint for contemporary studies of the microbiomes.
microbiomejournal.biomedcentral.com/articles/10....

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...

Sawhney et al. followed 52 infants from birth to age 8, uncovering how gut microbiomes shift, stabilize, and evolve. A key finding: the emergence and timing of Bacteroides- and Prevotella-dominated enterotypes. 👶🧬 1/n

Principles of gut microbiota assembly The gut microbiota plays a critical role in human health, yet its taxonomic complexity, interpersonal variability, and resistance to change in adulthood present challenges for understanding the factors driving shifts in its composition and function. Here,…

Principles of gut microbiota assembly

Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants - Microbiome Background The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcome...

Minimal lasting gut microbiome perturbation after antibiotic (amoxicillin) treatment in children, which mostly affected bifidobacteria: microbiomejournal.biomedcentral.com/articles/10....

Microbiota assembly in SPF mice: rdcu.be/d9yMn - No bifidobacteria in neonatal mice, no clear maternal source of pioneer strains.

Maternal strain transfer to C-section infants appears to be delayed but not eliminated, as infants at age 2-10y share similar strain numbers with their mothers and fathers as vaginally delivered infants. (4/4)

Maternal strain transfer is reduced if mothers had antibiotics and/or C-section. C-section infants follow altered trajectory of microbiota maturation and exhibit delayed a transition from an oxygen-tolerant to intolerant species-dominated microbiota. (3/4)

Mostly intestinal maternal strains from Bacteroides spp. and Bifidobacterium spp. transfer to neonates during vaginal birth and persist into infancy; strains from Bacteroides spp. are even shared between parents and their grandparents. (2/4)

Metaanalysis by @podlesny.bsky.social of the neonatal #microbiome, maternal strain inheritance, and persistence into adolescence is out: doi.org/10.1016/j.ij.... We used our SameStr tool to identify and visualize shared strain networks. (1/4)

Great study + opportunity to repost old tweets about our related meta-analysis: www.sciencedirect.com/science/arti..., which was smaller + focused on maternal strain transmission but also early-life #microbiome maturation, incl. oxygen-tolerant to intolerant species-dominated microbiome transition.

Hi Jan, could you please add me too. Thanks!

Our findings indicate microbiome-based diagnostic and TRF-based therapeutic applications that should be tested in IBD. - Special thanks to our collaborator Axel Lorentz @unihohenheim.bsky.social and the Baden-Wuerttemberg Foundation for funding. (7/x)

Interestingly, reduced gut microbiota rhythmicity and compositional changes preceded colitis symptoms in IL-10-/- mice, allowing us to train a PLS-DA model to predict colitis onset for individual mice from one experiment, which performed well on mice from a different experiment. (6/x)

Yet time-restricted feeding (TRF) had positive effects on IL-10-/- mice: It delayed colitis onset, reduced intestinal inflammation, improved the intestinal clock and increased gut microbiota rhythmicity - of the same taxa and to the same level as in wt mice. (5/x)

We found that while altered light/dark conditions disrupted the intestinal clock of wt mice, the intestinal clock and gut microbiota rhythmicity of IL-10-/- mice were impaired irrespective of external clock disruption, possibly due to dysbiosis even before the onset of colitis. (4/x)

We studied those questions in co-housed wt and IL-10-/- mice using altered light/dark cycles to disrupt and time-restricted feeding (TRF) to restore circadian rhythmicity. (3/x)

Could lifestyle (shift work, dietary habits) interfere with our biological clock, disrupt microbiota rhythmicity and promote intestinal inflammation and IBD? Could we improve clock, microbiota and inflammation with intermittent fasting? (2/x)

The gut microbiota predicts and time-restricted feeding delays experimental colitis The etiology of inflammatory bowel disease (IBD) remains unclear, treatment options unsatisfactory and disease development difficult to predict for individual patients. Dysbiosis of the gastrointes...

“The gut microbiota predicts and time-restricted feeding delays experimental colitis” New paper out from our group in GutMicrobes: www.tandfonline.com/doi/full/10..... Congratulations to first authors Hannah Ruple and Eva Haasis. (1/x)