Antibiotic tolerance: targeting bacterial survival DOI Creative Commons
Lucas Boeck

Current Opinion in Microbiology, Год журнала: 2023, Номер 74, С. 102328 - 102328

Опубликована: Май 26, 2023

Antimicrobial susceptibility testing is the cornerstone of antibiotic treatments. Yet, active drugs are frequently unsuccessful in vivo and most clinical trials investigating antibiotics fail. So far, bacterial survival strategies, other than drug resistance, have been largely ignored. As such, tolerance persisters, allowing populations to survive during treatments, could fill a gap testing. Therefore, it remains critical establish robust scalable viability measures define relevance survivors across various infections. If successful, these tools improve design development prevent formation or target survivors, ultimately reduce treatment failures curb resistance evolution.

Язык: Английский

Cross-feeding in the gut microbiome: Ecology and mechanisms DOI Creative Commons
Elizabeth J. Culp, Andrew L. Goodman

Cell Host & Microbe, Год журнала: 2023, Номер 31(4), С. 485 - 499

Опубликована: Апрель 1, 2023

Язык: Английский

Процитировано

139
The Mechanism of Bacterial Resistance and Potential Bacteriostatic Strategies DOI Creative Commons
Fusheng Zhang, Wei Cheng

Antibiotics, Год журнала: 2022, Номер 11(9), С. 1215 - 1215

Опубликована: Сен. 8, 2022

Bacterial drug resistance is rapidly developing as one of the greatest threats to human health. Bacteria will adopt corresponding strategies crack inhibitory effect antibiotics according antibacterial mechanism antibiotics, involving mutation target, secreting hydrolase, and discharging out cells through an efflux pump, etc. In recent years, bacteria are found constantly evolve new mechanisms including target protective protein, changes in cell morphology, so on, endowing them with multiple defense systems against leading emergence multi-drug resistant (MDR) unavailability drugs clinics. Correspondingly, researchers attempt uncover mystery bacterial develop more convenient effective strategies. Although traditional still play a significant role treatment diseases caused by sensitive pathogenic bacteria, they gradually lose efficacy MDR bacteria. Therefore, highly compounds, such phage therapy CRISPER-Cas precision therapy, gaining increasing amount attention, considered be treatments moist potential regard future. this review, nine identified summarized, which enhance retention rate under action promote distribution drug-resistant (DRB) population. Afterwards, three kinds methods introduced, compounds exhibit broad application prospects different mechanisms, has been successfully applied infectious super technology can edit genes at gene level, high accuracy flexibility. These provide options for clinical treatment, greatly alleviate current crisis.

Язык: Английский

Процитировано

98
Metabolic exchanges are ubiquitous in natural microbial communities DOI
Christian Kost, Kiran Raosaheb Patil, Jonathan Friedman

и другие.

Nature Microbiology, Год журнала: 2023, Номер 8(12), С. 2244 - 2252

Опубликована: Ноя. 23, 2023

Язык: Английский

Процитировано

83
Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling DOI Creative Commons
Zhepu Ruan, Kai Chen,

Weimiao Cao

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 1, 2024

Abstract Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within are largely unknown, and practical principles tools microbiome engineering still lacking. Here, we present a combinatory top-down bottom-up framework to engineer the construction of function-enhanced synthetic microbiomes. We show that application herbicide herbicide-degrader inoculation drives convergent succession different toward functional (e.g., enhanced bioremediation herbicide-contaminated soils). develop modeling pipeline, SuperCC, can be used document simulate performances Using construct bioremediation-enhanced based on 18 keystone species identified from Our results highlight importance in shaping functions provide guidance

Язык: Английский

Процитировано

37
Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback DOI Creative Commons
Joaquı́n Gutiérrez, Sant Kumar, Mustafa Khammash

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Авг. 16, 2022

Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies synthetic biology bioproduction. However, the difficulty controlling composition microbial consortia over time hinders their optimal use many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements computer-controlled optogenetic modulation bacterial growth to implement precise robust compositional control two-strain E. coli community. In addition, develop general framework dynamic modeling genetic circuits physiological context host-aware model determine parameters our closed-loop system. Our succeeds stabilizing strain ratio multiple parallel co-cultures at arbitrary levels changing these targets time, opening door implementation programs communities.

Язык: Английский

Процитировано

56
Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan DOI Creative Commons
Clara Correia‐Melo, Stephan Kamrad, Roland Tengölics

и другие.

Cell, Год журнала: 2023, Номер 186(1), С. 63 - 79.e21

Опубликована: Янв. 1, 2023

Metabolism is deeply intertwined with aging. Effects of metabolic interventions on aging have been explained intracellular metabolism, growth control, and signaling. Studying chronological in yeast, we reveal a so far overlooked property that influences via the exchange metabolites. We observed metabolites exported by young cells are re-imported chronologically cells, resulting cross-generational interactions. Then, used self-establishing metabolically cooperating communities (SeMeCo) as tool to increase metabolite significant lifespan extensions. The longevity SeMeCo was attributable reconfigurations methionine consumer cells. These obtained more glycolytic metabolism increased export protective turn extended supplied them methionine. Our results establish interactions determinant cellular show can shape environment extend their lifespan.

Язык: Английский

Процитировано

37
Antifungal Tolerance and Resistance Emerge at Distinct Drug Concentrations and Rely upon Different Aneuploid Chromosomes DOI Creative Commons
Feng Yang, Eduardo Scopel Ferreira da Costa, Hao Li

и другие.

mBio, Год журнала: 2023, Номер 14(2)

Опубликована: Март 6, 2023

Antifungal drug tolerance differs from resistance: tolerant cells grow slowly in drug, while resistant usually well, due to mutations a few known genes. More than half of Candida albicans clinical isolates have higher at body temperature they do the lower temperatures used for most lab experiments.

Язык: Английский

Процитировано

35
Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs DOI Creative Commons
Zhecheng Zhou, Linlin Zhuo, Xiangzheng Fu

и другие.

Briefings in Bioinformatics, Год журнала: 2023, Номер 25(1)

Опубликована: Ноя. 22, 2023

Abstract Exploring microbial stress responses to drugs is crucial for the advancement of new therapeutic methods. While current artificial intelligence methodologies have expedited our understanding potential drugs, models are constrained by imprecise representation microbes and drugs. To this end, we combine deep autoencoder subgraph augmentation technology first time propose a model called JDASA-MRD, which can identify indistinguishable In JDASA-MRD model, begin feeding established similarity matrices microbe drug into autoencoder, enabling extract robust initial features both Subsequently, employ MinHash HyperLogLog algorithms account intersections cardinality data between subgraphs, thus deeply extracting multi-hop neighborhood information nodes. Finally, integrating node with topological information, leverage graph neural network predict microbes’ offering more effective solution ’over-smoothing’ challenge. Comparative analyses on multiple public datasets confirm that model’s performance surpasses state-of-the-art models. This research aims offer profound insight adaptability furnish pivotal guidance treatment strategies. Our code publicly available at: https://github.com/ZZCrazy00/JDASA-MRD.

Язык: Английский

Процитировано

24
Interkingdom interactions between Pseudomonas aeruginosa and Candida albicans affect clinical outcomes and antimicrobial responses DOI
Lisa Juliane Kahl,

Nina Stremmel,

M. Alejandra Esparza-Mora

и другие.

Current Opinion in Microbiology, Год журнала: 2023, Номер 75, С. 102368 - 102368

Опубликована: Сен. 6, 2023

Язык: Английский

Процитировано

23
Taxonomic and environmental distribution of bacterial amino acid auxotrophies DOI Creative Commons
Josep Ramoneda, Thomas Bygh Nymann Jensen, Morgan N. Price

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Ноя. 22, 2023

Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify prevalence of amino acid auxotrophies across a broad diversity bacteria and habitats. We predicted biosynthetic capabilities 26,277 unique bacterial genomes spanning 12 phyla using metabolic pathway model validated with empirical data. Amino auxotrophy is widespread phyla, but conservatively estimate that majority taxa (78.4%) able all acids. Our estimates indicate more prevalent among obligate intracellular parasites in free-living genomic attributes characteristic 'streamlined' life history strategies. communities found habitats investigate environmental associations auxotrophy, data compiled from 3813 samples major aquatic, terrestrial, engineered environments. Auxotrophic were abundant host-associated environments (including human oral cavity gut) fermented food products, auxotrophic being relatively rare soil aquatic systems. Overall, work contributes complete understanding tree ecological contexts which can be successful strategy.

Язык: Английский

Процитировано

22