Karoline Faust
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View article: Growth stage and interspecies interactions shape the cell biology and cell cycle characteristics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis
Growth stage and interspecies interactions shape the cell biology and cell cycle characteristics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis Open
The human gut is a densely populated environment where microbial cells face frequent nutrient fluctuations. While previous studies have identified changes in gene expression, protein concentrations, and metabolite levels, less is known abo…
View article: Differential recovery of chain-elongating bacteria: comparing droplet, plating, and dilution-to-extinction methods
Differential recovery of chain-elongating bacteria: comparing droplet, plating, and dilution-to-extinction methods Open
Microbial chain elongation via reverse β-oxidation offers a more sustainable route to produce medium-chain fatty acids like caproate, commodity chemicals typically produced via (petro)chemical processes. Thermophilic anaerobic microbiomes …
View article: PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets
PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets Open
PlasticEnz is a new open-source tool for detecting plastic-degrading enzymes (plastizymes) in metagenomic data by combining sequence homology-based search with machine learning. It integrates custom Hidden Markov Models, DIAMOND alignments…
View article: μGrowthDB: querying, visualizing, and sharing microbial growth curve data
μGrowthDB: querying, visualizing, and sharing microbial growth curve data Open
Microbial growth curve data contain valuable information about microorganisms’ physiology and metabolism. However, they are currently reported in various formats scattered across publications. A generic resource that allows querying and co…
View article: microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis
microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis Open
Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag , a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched w…
View article: Discovery of alternative stable states in a synthetic human gut microbial community
Discovery of alternative stable states in a synthetic human gut microbial community Open
Several human-associated microbial communities exist in multiple configurations and can change their composition in response to perturbations, remaining in an altered state even after the perturbation ends. Multistability has been previous…
View article: Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes
Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes Open
Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities—shedding light on cell-to-cell variability in gene expression, regulatory dynamics, and metabolic potential. These approaches h…
View article: Effects of microplastics on <i>Daphnia</i> -associated microbiomes in situ and in vitro
Effects of microplastics on <i>Daphnia</i> -associated microbiomes in situ and in vitro Open
Microplastic pollution in aquatic environments is a growing global concern. Microplastics, defined as plastic fragments smaller than 5 mm, accumulate in freshwater reservoirs, especially in urban areas, impacting resident biota. This study…
View article: Discovery of alternative stable states in a synthetic human gut microbial community
Discovery of alternative stable states in a synthetic human gut microbial community Open
Several human-associated microbial communities exist in multiple configurations and can change their composition in response to perturbations, remaining in an altered state even after the perturbation ends. Multistability has been previous…
View article: How can concepts from ecology enable insights about cellular communities?
How can concepts from ecology enable insights about cellular communities? Open
View article: How can concepts from ecology enable insights about cellular communities?
How can concepts from ecology enable insights about cellular communities? Open
View article: Exploiting gut microbial traits and trade-offs in microbiome-based therapeutics
Exploiting gut microbial traits and trade-offs in microbiome-based therapeutics Open
View article: The impact of ecological memory on microbial community dynamics
The impact of ecological memory on microbial community dynamics Open
Ecological memory refers to the influence of past events on an ecosystem’s response to external or endogenous changes. Whereas memory’s contribution to ecosystem dynamics is well recognized, its role in microbial community dynamics has gai…
View article: Starvation responses impact interaction dynamics of human gut bacteria<i>Bacteroides thetaiotaomicron</i>and<i>Roseburia intestinalis</i>
Starvation responses impact interaction dynamics of human gut bacteria<i>Bacteroides thetaiotaomicron</i>and<i>Roseburia intestinalis</i> Open
Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact…
View article: starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis
starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis Open
Scripts to reproduce the counting of FC cells with: bit.ly/3WNrslL
View article: Starvation responses impact interaction dynamics of human gut bacteria<i>Bacteroides thetaiotaomicron</i>and<i>Roseburia intestinalis</i>
Starvation responses impact interaction dynamics of human gut bacteria<i>Bacteroides thetaiotaomicron</i>and<i>Roseburia intestinalis</i> Open
Bacterial growth often alters the environment, which in turn can impact interspecies interactions among bacteria. Here, we used an in vitro batch system containing mucin beads to emulate the dynamic host environment and to study its impact…
View article: Isolation and characterization of a thermophilic chain elongating bacterium that produces the high commodity chemical n-caproate from polymeric carbohydrates
Isolation and characterization of a thermophilic chain elongating bacterium that produces the high commodity chemical n-caproate from polymeric carbohydrates Open
View article: Tick microbial associations at the crossroad of horizontal and vertical transmission pathways
Tick microbial associations at the crossroad of horizontal and vertical transmission pathways Open
View article: Tick microbial associations at the crossroad of horizontal and vertical transmission pathways
Tick microbial associations at the crossroad of horizontal and vertical transmission pathways Open
Background: Microbial communities can affect disease risk by interfering with the transmission or maintenance of pathogens in blood-feeding arthropods. Here, we investigated whether bacterial communities vary between Ixodes ricinus nymphs,…
View article: Exploring the dynamics of a synthetic riverine bacterial community
Exploring the dynamics of a synthetic riverine bacterial community Open
The dynamics of a community of four planktonic bacterial strains isolated from river water was followed in R2 broth for 72 h in batch experiments. 16S rRNA gene sequencing and flow cytometry analyses were combined to monitor the change in …
View article: Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification
Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification Open
A bottleneck for microbial community experiments with many samples and/or replicates is the fast quantification of individual taxon abundances, which is commonly achieved through sequencing marker genes such as the 16S rRNA gene. Here, we …
View article: Additional file 1 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus
Additional file 1 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus Open
Additional file 1: Table S1. Metadata for all of the locations including their full names and coordinates as well as information on vegetation and tick density. Table S2. Number of samples collected from different tick life stages at diffe…
View article: Additional file 3 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus
Additional file 3 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus Open
Additional file 3: Table S4. Read counts for different taxa, including taxonomy per sample. Negative control samples included. Figure S1. Ordination of community composition with uncorrected abundances. Figure S2. Rarefaction curve of samp…
View article: Isolation and Characterization of a Thermophilic Chain Elongating Bacterium that Produces the High Commodity Chemical N-Caproate from Polymeric Carbohydrates
Isolation and Characterization of a Thermophilic Chain Elongating Bacterium that Produces the High Commodity Chemical N-Caproate from Polymeric Carbohydrates Open
View article: Additional file 4 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus
Additional file 4 of Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus Open
Additional file 4: Table S5. Results of PERMANOVA testing an effect of tick life stage on community variation, and the analysis of variance. Table S6. Results of models of stage explaining Rickettsia and Rickettsiella abundance. Table S7. …
View article: Additional file 1 of Tick microbial associations at the crossroad of horizontal and vertical transmission pathways
Additional file 1 of Tick microbial associations at the crossroad of horizontal and vertical transmission pathways Open
Additional file 1: Table S1. Details on studied forest sites. Table S2. The qPCR protocol for detection of tick symbionts and pathogens. Table S3. Bacterial loads of samples for the 16S rRNA sequencing; sample scheme. Table S4. Details on …
View article: Fast and flexible analysis of linked microbiome data with mako
Fast and flexible analysis of linked microbiome data with mako Open
View article: Correction to: Disentangling environmental effects in microbial association networks
Correction to: Disentangling environmental effects in microbial association networks Open
View article: Temporal variability in quantitative human gut microbiome profiles and implications for clinical research
Temporal variability in quantitative human gut microbiome profiles and implications for clinical research Open
View article: Quantifying the impact of ecological memory on the dynamics of interacting communities
Quantifying the impact of ecological memory on the dynamics of interacting communities Open
Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, ye…