Cross-feeding in the gut microbiome: ecology and mechanisms

EJ Culp, AL Goodman - Cell host & microbe, 2023 - cell.com
Microbial communities are shaped by positive and negative interactions ranging from
competition to mutualism. In the context of the mammalian gut and its microbial inhabitants …

Metabolic exchanges are ubiquitous in natural microbial communities

C Kost, KR Patil, J Friedman, SL Garcia… - Nature Microbiology, 2023 - nature.com
Microbial communities drive global biogeochemical cycles and shape the health of plants
and animals—including humans. Their structure and function are determined by ecological …

Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback

J Gutiérrez Mena, S Kumar, M Khammash - Nature Communications, 2022 - nature.com
Communities of microbes play important roles in natural environments and hold great
potential for deploying division-of-labor strategies in synthetic biology and bioproduction …

The mechanism of bacterial resistance and potential bacteriostatic strategies

F Zhang, W Cheng - Antibiotics, 2022 - mdpi.com
Bacterial drug resistance is rapidly developing as one of the greatest threats to human
health. Bacteria will adopt corresponding strategies to crack the inhibitory effect of antibiotics …

Myxobacteria restrain Phytophthora invasion by scavenging thiamine in soybean rhizosphere via outer membrane vesicle-secreted thiaminase I

C Xia, Y Zhao, L Zhang, X Li, Y Cheng, D Wang… - Nature …, 2023 - nature.com
Public metabolites such as vitamins play critical roles in maintaining the ecological functions
of microbial community. However, the biochemical and physiological bases for fine-tuning of …

Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC

S Kamrad, C Correia-Melo, L Szyrwiel, SK Aulakh… - Nature …, 2023 - nature.com
Genetically identical cells are known to differ in many physiological parameters such as
growth rate and drug tolerance. Metabolic specialization is believed to be a cause of such …

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

J Ramoneda, TBN Jensen, MN Price… - Nature …, 2023 - nature.com
Many microorganisms are auxotrophic—unable to synthesize the compounds they require
for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a …

Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs

Z Zhou, L Zhuo, X Fu, Q Zou - Briefings in Bioinformatics, 2024 - academic.oup.com
Exploring microbial stress responses to drugs is crucial for the advancement of new
therapeutic methods. While current artificial intelligence methodologies have expedited our …

Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions

J Chen, SL Siliceo, Y Ni, HB Nielsen, A Xu… - Microbiome, 2023 - Springer
Background A growing body of evidence suggests that the gut microbiota is strongly linked
to general human health. Microbiome-directed interventions, such as diet and exercise, are …

Interkingdom interactions between Pseudomonas aeruginosa and Candida albicans affect clinical outcomes and antimicrobial responses

LJ Kahl, N Stremmel, MA Esparza-Mora… - Current Opinion in …, 2023 - Elsevier
Infections that involve interkingdom microbial communities, such as those between bacteria
and yeast pathogens, are difficult to treat, associated with worse patient outcomes, and may …