Metabolic synergy and complementarity in the Ips typographus holobiont DOI Creative Commons
Zaki Saati‐Santamaría, Martin Kostovčík, Tereza Veselská

и другие.

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

Abstract Microbial symbiosis plays a central role in shaping ecological and evolutionary processes, driving the adaptation of host organisms to challenging environments. However, mechanisms underlying functional integration metabolic cooperation within holobionts remain poorly understood. Current research often emphasizes taxonomic composition microbiomes, but interactions that sustain these associations are less explored, especially nutrient-poor ecosystems. This study addresses this knowledge gap by investigating interdependencies gut microbiome European spruce bark beetle (Ips typographus, ESBB). Using meta-transcriptomic analyses, we reveal critical contributions bacterial fungal symbionts facilitating survival. Our findings show microbial partners compensate for deficiencies, with cross-kingdom enabling biosynthesis essential nutrients such as amino acids vitamins. Furthermore, division labor among taxa is evident, bacteria primarily degrading plant polymers xylan pectin, fungi specializing glucan degradation. Functional redundancy key pathways suggests an adaptive mechanism ensure nutrient availability under fluctuating community composition. In addition, identify previously unappreciated pathway nitrogen acquisition via oxidation inorganic nitrogen. highlight importance their success symbiotic associations. results provide framework exploring cycling resource use.

Язык: Английский

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
A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities DOI Creative Commons
Huadong Peng, Alexander P. S. Darlington, Eric J. South

и другие.

Nature Microbiology, Год журнала: 2024, Номер 9(3), С. 848 - 863

Опубликована: Фев. 7, 2024

Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic overexpression yeast strains that can be used to create through exchange essential metabolites. Using these as modules, engineered two- three-member using different cross-feeding architectures. Through a combination ensemble modelling experimentation, explored how cellular (for example, metabolite strength) environmental initial population ratio, density extracellular supplementation) factors govern dynamics in systems. We tested use toolkit division labour case study show it enables tuneable antioxidant resveratrol production. expect this become useful resource variety applications synthetic ecology biomanufacturing.

Язык: Английский

Процитировано

21
Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome DOI
Grégoire Michoud, Hannes Peter, Susheel Bhanu Busi

и другие.

Nature Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 2, 2025

Язык: Английский

Процитировано

2
Metabolic complexity drives divergence in microbial communities DOI
Michael Silverstein, Jennifer Bhatnagar, Daniel Segrè

и другие.

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(8), С. 1493 - 1504

Опубликована: Июль 2, 2024

Язык: Английский

Процитировано

9
Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks DOI Creative Commons
Xi Peng,

Shang Wang,

Miaoxiao Wang

и другие.

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

Опубликована: Сен. 17, 2024

Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and complementarity networks. We apply this approach temperature gradient hot spring, unraveling the interplay between thermal stress cooperation. Our analysis reveals an increase in frequency of with rising temperatures. Amino acids, coenzyme A derivatives, carbohydrates emerge as key exchange metabolites, forming foundation for syntrophic which commensalistic take greater proportion than mutualistic ones. These exchanges are most prevalent phylogenetically distant species, especially archaea-bacteria collaborations, crucial adaptation harsh environments. Furthermore, identify significant positive correlation basal metabolite genome size disparity, potentially signifying means streamlined leverage cooperation metabolically richer partners. This phenomenon is also confirmed another composting system has similar wide range fluctuations. provides feasible way decipher mechanisms underlying microbial interactions, our findings suggested environmental regulates cooperative strategies thermophiles, while dependencies have been hardwired into their during co-evolutions.

Язык: Английский

Процитировано

9
Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth DOI Creative Commons
Nan Yang,

Henriette Lyng Røder,

Wisnu Adi Wicaksono

и другие.

The ISME Journal, Год журнала: 2024, Номер 18(1)

Опубликована: Янв. 1, 2024

Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within communities established on roots. Here, a well-established four-species model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis study impact of growth community dynamics SPMX co-culture notably promoted root development biomass. Co-cultured increased colonization formed biofilms, structurally different from those by monocultures. By combining 16S rRNA gene amplicon sequencing fluorescence situ hybridization with confocal laser scanning microscopy, we found that composition significantly changed over time. Monoculture P. amylolyticus colonized poorly, but its population were highly enhanced when residing biofilm. Exclusion reduced overall production three species, resulting loss growth-promoting effects. Combined analysis, this led identification keystone species. Our findings highlight weak colonizers may benefit mutualistic complex hereby become important species impacting function. This work expands knowledge uncovering interspecific roots, beneficial for harnessing mutualism promoting growth.

Язык: Английский

Процитировано

8
Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria DOI Creative Commons
Junbo Tang, Wenlong Zuo,

Lizhen Guo

и другие.

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

Опубликована: Авг. 13, 2024

The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro vivo, provides complementary demethylation service to promote growth on methylated homogalacturonan, an enriched polysaccharide pectin. In exchange, shares digestive products with Bifidobacterium, through which positive established. This vanishes when not required non-methylated diet. Results from biochemical gene expression analyses combined model simulation further suggest that ratio change major homogalacturonan breakdown products, galacturonic acid (GalA) di-GalA, determines bacterial interaction. study unravels glycan metabolism may shape Microbial honey bee are incompletely understood. authors report reciprocal core genera: aids pectin backbone enabling its by Gilliamella; return, digestion products.

Язык: Английский

Процитировано

8
Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation DOI Creative Commons
Xingsheng Yang, Kai Feng, Shang Wang

и другие.

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Сен. 7, 2024

Язык: Английский

Процитировано

8
Dynamically induced spatial segregation in multispecies bacterial bioconvection DOI Creative Commons

Óscar Adrián Gallardo-Navarro,

Rinat Arbel‐Goren, Elias August

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 22, 2025

Active matter, from motile bacteria to animals, can exhibit striking collective and coherent behavior. Despite significant advances in understanding the behavior of homogeneous systems, little is known about self-organization dynamics heterogeneous active such as complex diverse bacterial communities. Under oxygen gradients, many species swim towards air-liquid interfaces auto-organized, directional bioconvective flows, whose spatial scales exceed cell size by orders magnitude. Here we show that multispecies suspensions undergoing oxytactic-driven bioconvection dynamically driven segregation, despite enhanced mixing fact these coexist their natural habitat. Segregation observed patterns spatially interlocked domains, with local dominance one constituent suspension. Our findings suggest segregation mechanisms are species-specific behaviors under conditions hydrodynamic flow, rather than biochemical repulsion. Thus, different characteristics same ecological context enhance access limiting resources. This work provides novel insights on role heterogeneity well microbial communities, organization Heterogeneous including often forms environmental yet remain poorly understood. study reveals enhancing resource coexistence shared habitats.

Язык: Английский

Процитировано

1
Harnessing microbial division of labor for biomanufacturing: a review of laboratory and formal modeling approaches DOI Creative Commons
Fatima Ceballos Rodriguez-Conde, S. Zhu, Duygu Dikicioǧlu

и другие.

Critical Reviews in Biotechnology, Год журнала: 2025, Номер unknown, С. 1 - 19

Опубликована: Фев. 19, 2025

Bioprocess industries aim to meet the increasing demand for product complexity by designing enhanced cellular and metabolic capabilities host. Monocultures, standard biomanufacturing workhorses, are often restricted in their capability these demands, solution involves genetic modification of Synthetic microbial communities a promising alternative monocultures because they exhibit division labor, enabling efficient resource utilization pathway modularity. This specialization minimizes burden enhances robustness perturbations, providing competitive advantage. Despite this potential, biotechnological or bioprocessing applications remains limited. The recent emergence new innovative community design tools strategies, particularly those harnessing holds promise change outlook. Understanding interactions governing natural can be used identify complementary partners, informing synthetic design. Therefore, we consider engineering labor as viable accelerate progress field. review presents current understanding how enable information perform tasks otherwise unfeasible individual organisms. We then evaluate laboratory formal modeling approaches specifically developed to: elucidate physiology, guide experimental design, improve our complex assisting By synthesizing insights, present comprehensive framework that advances use applications.

Язык: Английский

Процитировано

1