Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades DOI Creative Commons
Ruirui Chen, Dong Yang, Emily Graham

et al.

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 21, 2023

Abstract The eco-evolutionary tradeoff between microbial mitigation of carbon limitation and maintenance functional traits in saline soils, a habitat rapidly expanding extent under climate change, represents significant knowledge gap predicting future soil health ecological function. Through shotgun metagenomic sequencing coastal soils along salinity gradient, we show contrasting directions bacteria archaea that manifest changes to genome size potential the microbiome with increasing stress. Bacteria exhibited reduced sizes associated depletion core metabolic genes response salinity, while displayed larger genomes an enrichment salt-resistance, genes, especially enhanced capacity for acquisition soils. This suggests conserve energy through streamlining when facing salt stress, invest pathways broaden their resource usage. These findings suggest divergent patterns adaptations stress amongst clades serve as foundation understanding microbiomes escalating change.

Language: Английский

Antibiotic perturbations to the gut microbiome DOI
Skye R. S. Fishbein, Bejan Mahmud, Gautam Dantas

et al.

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 21(12), P. 772 - 788

Published: July 25, 2023

Language: Английский

Citations

174
Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades DOI Creative Commons
Yang Dong, Ruirui Chen, Emily Graham

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 17, 2024

Abstract With the continuous expansion of saline soils under climate change, understanding eco-evolutionary tradeoff between microbial mitigation carbon limitation and maintenance functional traits in represents a significant knowledge gap predicting future soil health ecological function. Through shotgun metagenomic sequencing coastal along salinity gradient, we show contrasting directions bacteria archaea that manifest changes to genome size potential microbiome. In salt environments with high requirements, exhibit reduced sizes associated depletion metabolic genes, while display larger genomes enrichment salt-resistance, metabolic, carbon-acquisition genes. This suggests conserve energy through streamlining when facing stress, invest pathways broaden their resource usage. These findings suggest divergent adaptations stress amongst clades serve as foundation for response microbiomes escalating change.

Language: Английский

Citations

18
Antibiotic resistance in bacterial communities DOI Creative Commons
Marlis Denk-Lobnig, Kevin B. Wood

Current Opinion in Microbiology, Journal Year: 2023, Volume and Issue: 74, P. 102306 - 102306

Published: April 11, 2023

Language: Английский

Citations

36
CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater DOI

Moran Tang,

Qian Chen, Haohui Zhong

et al.

Water Research, Journal Year: 2024, Volume and Issue: 251, P. 121137 - 121137

Published: Jan. 21, 2024

Language: Английский

Citations

14
Cooperative growth in microbial communities is a driver of multistability DOI Creative Commons
William Lopes, Daniel R. Amor, Jeff Gore

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 3, 2024

Abstract Microbial communities often exhibit more than one possible stable composition for the same set of external conditions. In human microbiome, these persistent changes in species and abundance are associated with health disease states, but drivers alternative states remain unclear. Here we experimentally demonstrate that a cross-kingdom community, composed six relevant to respiratory tract, displays four each dominated by different species. pairwise coculture, observe widespread bistability among pairs, providing natural origin multistability full community. contrast common association between antagonism, experiments reveal many positive interactions within community members. We find multiple display cooperative growth, modeling predicts this could drive observed as well non-canonical outcomes. A biochemical screening reveals glutamate either reduces or eliminates cooperativity growth several species, confirm such supplementation extent across pairs Our findings provide mechanistic explanation how rather competitive can underlie microbial communities.

Language: Английский

Citations

12
Risk assessment and dissemination mechanism of antibiotic resistance genes in compost DOI Creative Commons
Yifei Xu, Lin Zhu,

Shanguo Chen

et al.

Environment International, Journal Year: 2023, Volume and Issue: 178, P. 108126 - 108126

Published: Aug. 1, 2023

In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted accumulation residual antibiotic resistance genes (ARGs) manure. Composting, as a crucial approach for utilization manure resources, potential to reduce levels ARGs manure, although complete elimination is challenging. Previous studies have primarily focused on diversity abundance compost or solely examined correlation between their carriers, potentially leading misjudgment actual risk associated with compost. To address this gap, study investigated transfer co-occurrence opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data worldwide. The results demonstrated that was significantly lower than suggesting composting effectively reduces ARGs. Further analysis showed microbes shifted life history strategy due pressure formed metabolic interactions dominated antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without addition recommended control evolution, dissemination, abatement both at source throughout processing.

Language: Английский

Citations

19
Natural defence mechanisms of electrochemically active biofilms: From the perspective of microbial adaptation, survival strategies and antibiotic resistance DOI
Teng Cai,

Yule Han,

Jiayi Wang

et al.

Water Research, Journal Year: 2024, Volume and Issue: 262, P. 122104 - 122104

Published: July 14, 2024

Language: Английский

Citations

6
Fitness Costs of Antibiotic Resistance Impede the Evolution of Resistance to Other Antibiotics DOI Creative Commons
Farhan Rahman Chowdhury, Brandon Findlay

ACS Infectious Diseases, Journal Year: 2023, Volume and Issue: 9(10), P. 1834 - 1845

Published: Sept. 19, 2023

Antibiotic resistance is a major threat to global health, claiming the lives of millions every year. With nearly dry antibiotic development pipeline, novel strategies are urgently needed combat resistant pathogens. One emerging strategy use sequential therapy, postulated reduce rate at which evolves. Here, we soft agar gradient evolution (SAGE) system carry out high-throughput in vitro bacterial against pressure. We find that chloramphenicol (CHL) severely affects fitness, slowing antibiotics nitrofurantoin and streptomycin emerges. In acquisition compensatory mutations CHL-resistant cells markedly improves fitness adaptation rates but fails restore wild-type levels streptomycin. Genome sequencing reveals distinct evolutionary paths fitness-impaired populations, suggesting trade-offs favor mitigation costs. show speed fronts SAGE plates reliable indicator trajectories resistance. Identification whose mutational mechanisms confer stable impairments may help clinicians prescribe therapies less prone evolution.

Language: Английский

Citations

15
Modulation of antibiotic effects on microbial communities by resource competition DOI Creative Commons
Daniel Newton, Po-Yi Ho, Kerwyn Casey Huang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 26, 2023

Abstract Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models resource competition to investigate responses species-specific death rates, as induced by antibiotic activity or other growth-inhibiting factors such bacteriophages. Our analyses highlight complex dependence species coexistence that can arise from interplay and activity, independent biological mechanisms. In particular, identify structures cause richness depend order sequential application (non-transitivity), emergence synergistic antagonistic effects under simultaneous multiple (non-additivity). These behaviors be prevalent, especially when generalist consumers are targeted. Communities prone either synergism antagonism, typically not both, antagonism more common. Furthermore, a striking overlap in lead non-transitivity during sequences those non-additivity combination. sum, our results establish broadly applicable framework for predicting microbial dynamics deleterious perturbations.

Language: Английский

Citations

14
ATP burst is the dominant driver of antibiotic lethality in Mycobacterium smegmatis DOI Open Access

Tejan Lodhiya,

Aseem Palande,

Anjali Veeram

et al.

Published: Jan. 21, 2025

Antibiotic-tolerant bacteria, due to their unique physiology, are refractory antimicrobial killing and pose challenges for infection control. Incomplete knowledge of how bactericidal antibiotics work, limits our understanding partial resistance phenotypic tolerance in mycobacteria, a driver developing genetic resistance. Using proteomics, 13 C isotopomer analysis, biochemical assays, we investigated the physiological response M. smegmatis challenged with aminoglycoside fluoroquinolone antibiotics. Two distinct classes elicited remarkably similar responses increased flux through TCA cycle, causing enhanced respiration, ROS generation, ATP burst. We observed that excessive levels not ROS, dominantly contributes cidality, which may part be, conferred by sequestration divalent metal ions ATP. Consequently, isotope tracing indicated cycle deviation from its oxidative arm as bacterial adaptive mechanism, also included activated intrinsic higher propensity develop antibiotic Our study provides new intricate mechanisms antibiotic-induced cell death expands current paradigm action.

Language: Английский

Citations

0