At what cost? The impact of bacteriophage resistance on the growth kinetics and protein synthesis of Escherichia coli DOI Creative Commons
Lotta Landor, Jesslyn Tjendra, Kristin Erstad

и другие.

Environmental Microbiology Reports, Год журнала: 2024, Номер 16(6)

Опубликована: Ноя. 19, 2024

Abstract Cost of bacteriophage resistance (COR) is important in explaining processes diversification and coexistence microbial communities. COR can be expressed different traits, the lack universally applicable methods to measure fitness trade‐offs makes challenging study. Due its fundamental role growth, we explored protein synthesis as a target for quantifying COR. In this study, growth kinetics three genome‐sequenced strains phage‐resistant Escherichia coli , along with phage‐susceptible wild‐type, were characterized over range glucose concentrations. Bioorthogonal non‐canonical amino acid tagging (BONCAT) was used track differences synthetic activity between wild‐type E. . Two resistant strains, levels phage susceptibility, showed mucoid phenotypes corresponding mutations genes associated Rcs phosphorelay. These isolates, however, had reduced rates potentially lower activity. Another isolate mutational profile maintained same rate increased BONCAT fluorescence, but yield lower. Together, these findings present patterns resulting from phage‐induced demonstrate potential applicability tool measuring

Язык: Английский

Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient DOI
Xin Sun,

Ariel Favier,

Jacquelyn Folmar

и другие.

The American Naturalist, Год журнала: 2024, Номер 204(4), С. 381 - 399

Опубликована: Июнь 28, 2024

AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on assembly. In particular, microbial communities play a role ecosystem, but we do not understand how changing like temperature are going to affect composition or function. this article, studied self-assembly multiple synthetic environments changes based metabolic responses different functional groups along gradient. many communities, coexist through partitioning carbon sources an emergent trophic structure (cross-feeding). system, respirofermentative bacteria display preference for sugars supplied as only source secrete secondary (organic acids) that more efficiently consumed by obligate respirators. As consequence structure, plasticity respirofermenters has downstream consequences relative abundance respirators across temperatures. We found temperatures can largely be described increase fermentation by-products with increasing from bacteria. This research highlights importance trade-offs species interactions dynamics gradients.

Язык: Английский

Процитировано

4
Levels of microbial diversity affect the stability and function of dark fermentation bioreactors DOI Creative Commons
Marcelo Navarro-Díaz,

Valeria Aparicio-Trejo,

Idania Valdez‐Vazquez

и другие.

Frontiers in Industrial Microbiology, Год журнала: 2024, Номер 2

Опубликована: Апрель 25, 2024

Climate change and pollution drive the need for fossil fuel alternatives. Dark fermentation offers promise through use of microbial consortia to convert organic matter into hydrogen gas. Persisting challenges like instability low yields may stem from reduced diversity anaerobic digestion communities that serve as inoculum undergo aggressive pretreatments culturing conditions. This study explores impact loss on function, focusing biogas production stability. Two treatments, with without pretreatment, were tested 12 replicate bioreactors each, resulting in differing levels. Microbial assessed via 16S amplicon sequencing, monitoring production, volatile fatty acids, testing invasion susceptibility. The two treatments exhibited divergent assembly functional trajectories, although replicates within each treatment ultimately converged similar compositions stable levels production. Heat-treated showed a 91.5% increase but higher susceptibility compared non-treated. Non-treated unique species associations (e.g. Ethanoligenens harbinense Enterococcus olivae ), distinct commonly studied Clostridium group. These findings provide insights effects stability, elucidating differences across taxonomic stability well Moreover, identification novel bacterial groups associated suggests promising directions future research enhance control design dark fermentation.

Язык: Английский

Процитировано

3
Environmental exposures, the oral–lung axis and respiratory health: The airway microbiome goes on stage for the personalized management of human lung function DOI Creative Commons
Junkal Garmendia,

Pilar Cebollero‐Rivas

Microbial Biotechnology, Год журнала: 2024, Номер 17(6)

Опубликована: Июнь 1, 2024

The human respiratory system is constantly exposed to environmental stimuli, sometimes including toxicants, which can trigger dysregulated lung immune responses that lead symptoms, impaired function and airway diseases. Evidence supports the microbiome in lungs has an indispensable role health disease, acting as a local gatekeeper mediates interaction between cues health. Moreover, intimately intertwined with oral through oral-lung axis. Here, we discuss intricate three-way relationship (i) cigarette smoking, strong effects on microbial community structure of lung; (ii) dysbiosis disease cavity; (iii) its causal patients suffering chronic obstructive pulmonary (COPD), leading cause morbidity mortality worldwide. We highlight exciting outcomes arising from recently established interactions exposures, microbiome, metabolites-functional attributes host, well how these associations have potential predict status host index. For completion, argue incorporating (synthetic) ecology our contemporary understanding presents challenges also rises novel opportunities exploit axis towards innovative diagnostics, prognostics, patient stratification microbiota-targeted clinical interventions context current therapies.

Язык: Английский

Процитировано

3
The microbial-driven nitrogen cycle and its relevance for plant nutrition DOI
Hanna Koch, Angela Sessitsch

Journal of Experimental Botany, Год журнала: 2024, Номер 75(18), С. 5547 - 5556

Опубликована: Июнь 18, 2024

Abstract Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids proteins. Microorganisms are major drivers N-cycling processes in all ecosystems, including the soil plant environment. The availability N growth-limiting factor for plants it significantly affected by microbiome. Plants microorganisms form complex interaction networks resulting molecular signaling, exchange, other distinct metabolic responses. In these networks, microbial partners influence growth use efficiency either positively or negatively. Harnessing beneficial effects specific players within crop microbiomes promising strategy to counteract emerging threats human planetary health due overuse industrial fertilizers. However, addition N-providing activities (e.g. well-known symbiosis legumes Rhizobium spp.), plant–microorganism interactions must be considered obtain complete picture how microbial-driven transformations might affect nutrition. For this, we review recent insights into tight interplay between microorganisms, focusing on N-transformation representing sources sinks that ultimately shape acquisition.

Язык: Английский

Процитировано

3
Gradient boosted regression as a tool to reveal key drivers of temporal dynamics in a synthetic yeast community DOI Creative Commons
Cleo G. Conacher, Bruce W. Watson, Florian F. Bauer

и другие.

FEMS Microbiology Ecology, Год журнала: 2024, Номер 100(7)

Опубликована: Май 22, 2024

Microbial communities are vital to our lives, yet their ecological functioning and dynamics remain poorly understood. This understanding is crucial for assessing threats these systems leveraging biotechnological applications. Given that temporal linked community functioning, this study investigated the drivers of succession in wine yeast community. We experimentally generated population data used it create an interpretable model with a gradient boosted regression tree approach. The was trained on viable species populations various combinations, including pairs, triplets, quadruplets, evaluated predictive accuracy input feature importance. Key findings revealed inoculation dosage non-Saccharomyces significantly influences performance mixed cultures, while Saccharomyces cerevisiae consistently dominates regardless initial abundance. Additionally, we observed multispecies interactions where Wickerhamomyces anomalus were influenced by Torulaspora delbrueckii pairwise but interaction altered inclusion S. cerevisiae. provides insights into offers valuable machine learning-based analysis techniques applicable other microbial communities, opening new avenues harnessing communities.

Язык: Английский

Процитировано

2
Development of a Flavor-Oriented Synthetic Microbial Community for pour-over rice wine: A Comprehensive Microbial Community Analysis DOI
Qi Peng, Huajun Zheng,

Leping Quan

и другие.

Food Microbiology, Год журнала: 2024, Номер 126, С. 104677 - 104677

Опубликована: Ноя. 2, 2024

Язык: Английский

Процитировано

2
Niche formation and metabolic interactions result in stable diversity in a spatially structured cyanobacterial community DOI Creative Commons
Sarah J. N. Duxbury, Sébastien Raguideau,

Kelsey Cremin

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Дек. 13, 2022

ABSTRACT Understanding how microbial communities maintain stable compositional diversity is key for predicting community function. Studies from species pairwise interactions and synthetic indicate that metabolic spatial organisation can influence coexistence, but the relevance of these factors in more complex unclear. Model systems often lack multi-species complexity, thereby making it difficult to study temporally. Here we used a spatially-organised cyanobacterial enrichment investigate its stability. Over year passaging media without significant carbon source, found maintains relatively high diversity, with 17 co-existing bacterial species. Using short long read shotgun metagenomics sequencing different time point samples, have reconstructed complete genomes. Genomic annotation revealed complementary functions involving breakdown vitamin biosynthesis suggesting amongst members. isolated species, provide experimental support provision through slime growth on component substrates by representative members Proteobacteria Actinobacteriota phyla. Additionally, experimentally show uptake between prototrophic auxotrophic We also genomic capability (an)oxygenic photosynthesis sulfur cycling several consistent formation oxygen gradients across ‘photogranule’ structures, supporting niches sustain specific functions. These findings niche enable maintenance stability diversity. SIGNIFICANCE STATEMENT Microbes exist as species-diverse nature understanding their an open challenge ecology. established maintained spatially-organised, photosynthetic freshwater reservoir long-term culturing laboratory medium. this taxonomically-diverse set Combining physiological assays, characterised novel filamentous cyanobacterium capable carbohydrate-rich ‘slime’ secretion other microbes. predict inter-species exchanges identify alternative types are likely be favoured oxygen-free zones identified within structures. Our structures coexistence natural ecosystems.

Язык: Английский

Процитировано

8
Ecological dynamics explain modular denitrification in the ocean DOI Creative Commons
Xin Sun, Pearse Buchanan, Irene H. Zhang

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(52)

Опубликована: Дек. 18, 2024

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO 3 – →NO 2 →NO→N O→N ), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N O) production. Denitrification-derived N typically measured modeled as a single step, but observations reveal that most denitrifiers OMZs contain subsets (“modules”) of the complete pathway. Here, we identify ecological mechanisms sustaining diverse denitrifiers, explain prevalence certain modules, examine implications for loss. We describe microbial functional types carrying out modules by their underlying redox chemistry, constraining traits with thermodynamics pathway length penalties, an idealized ecosystem model. Biomass yields single-step increase along when organic matter (OM) limits growth, explains viability populations respiring NO O -filled ocean. Results predict denitrifier community succession environmental gradients: Pathway increases limiting substrate shifts from OM to N, suggesting niche short module free-living, OM-limited communities, particle-associated consistent observations. The model captures mechanistically observed dominance higher tolerance module. also capture dominant source O. Our framework advances mechanistic understanding relationship between ecology ocean can be extended other processes environments.

Язык: Английский

Процитировано

1
Editorial overview: Systems and synthetic biology of microbial cells and communities DOI
Victor Sourjik, Kiran Raosaheb Patil

Current Opinion in Microbiology, Год журнала: 2024, Номер 80, С. 102517 - 102517

Опубликована: Июль 18, 2024

Язык: Английский

Процитировано

0
At what cost? The impact of bacteriophage resistance on the growth kinetics and protein synthesis of Escherichia coli DOI Creative Commons
Lotta Landor, Jesslyn Tjendra, Kristin Erstad

и другие.

Environmental Microbiology Reports, Год журнала: 2024, Номер 16(6)

Опубликована: Ноя. 19, 2024

Abstract Cost of bacteriophage resistance (COR) is important in explaining processes diversification and coexistence microbial communities. COR can be expressed different traits, the lack universally applicable methods to measure fitness trade‐offs makes challenging study. Due its fundamental role growth, we explored protein synthesis as a target for quantifying COR. In this study, growth kinetics three genome‐sequenced strains phage‐resistant Escherichia coli , along with phage‐susceptible wild‐type, were characterized over range glucose concentrations. Bioorthogonal non‐canonical amino acid tagging (BONCAT) was used track differences synthetic activity between wild‐type E. . Two resistant strains, levels phage susceptibility, showed mucoid phenotypes corresponding mutations genes associated Rcs phosphorelay. These isolates, however, had reduced rates potentially lower activity. Another isolate mutational profile maintained same rate increased BONCAT fluorescence, but yield lower. Together, these findings present patterns resulting from phage‐induced demonstrate potential applicability tool measuring

Язык: Английский

Процитировано

0