The proteome is a terminal electron acceptor

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(1)

Published: Jan. 3, 2025

Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. Escherichia coli , for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation respiration. To understand the limits evolutionary consequences this metabolic flexibility, we developed a coarse-grained mathematical framework coupling chemistry with principles cellular resource allocation. Our models inherit key qualities both their antecedents: i) describing diverse chemistries ii) enforcing simultaneous balancing atom (e.g., carbon), electron, energy (adenosine triphosphate) flows, as models, while iii) treating product catalyst process, allocation models. Assembling integrated respiration, fermentation, photosynthesis clarified microbiological phenomena, including demonstrating that autotrophs more slowly than heterotrophs because constraints imposed by intracellular production carbon. model further predicted heterotrophic improved matching state nutrient environment. Through analysis ≈ 60,000 genomes proteomic datasets, found evidence proteins indeed accumulate amino acid substitutions promoting matching. We therefore propose an unexpected mode genome evolution where neutral or deleterious individual biochemical structural functions can nonetheless be selected due redox-chemical benefit population.

Language: Английский

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Adaptation of Archaeal Communities to Summer Hypoxia in the Sediment of Bohai Sea

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT Understanding the adaptation of archaea to hypoxia is essential for deciphering functions and mechanisms microbes when suffering environmental changes. However, dynamics responses sedimentary in Bohai Sea are still unclear. In this study, diversity, composition, distribution archaeal community sediment along an inshore–offshore transect across oxygen‐depleted area were investigated June, July, August 2021 by employing high‐throughput sequencing 16S rRNA gene. Results indicated that communities dominated Thermoproteota (80.61%), Asgardarchaeota (8.70%), Thermoplasmatota (5.27%). Dissolved oxygen (DO) NO 3 − two key factors shaping communities, accounting 49.5% 38.3% total variabilities ( p < 0.05), respectively. With intensity depletion, diversity increased significantly. Microbial networks revealed Bathyarchaeia played a role interacting with both bacteria other groups. Furthermore, adaptions also displayed variation relative abundance predicted ecological metabolic pathways. The enrichment specific nitrogen transformation enzymes showed potential fixation removal, which might contribute balance N budget thus facilitate restoration under eutrophication Sea. Our results provided new picture on archaea, will be beneficial further investigations extreme environments theoretically practically.

Language: Английский

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Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut

Gut Microbes, Journal Year: 2025, Volume and Issue: 17(1)

Published: March 16, 2025

In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This protection from is maintained interactions both within bacterial well with host. As consequence, plays critical role in various physiological processes including structure function of barrier, educating immune system, modulating motor, digestive/absorptive, neuroendocrine system all which are crucial for human health disease pathogenesis. Pre- probiotics, widely available clinically established, offer benefits primarily by beneficially microbiome. However, their clinical outcomes can vary significantly due to differences host physiology, diets, individual compositions, other factors. perspective paper highlights emerging scientific insights into importance micronutrient sharing, redox balance, keystone species, barrier diverse functional ecosystem, relevance health. We propose novel approach that targets ecosystems taxa performance supplying micronutrients form colon-delivered vitamins, precision prebiotics [e.g. milk oligosaccharides (HMOs) or synthetic glycans] components precisely tailored ingredient combinations optimize Such strategy may effectively support stabilize ecosystems, providing more robust consistent across individuals conditions, thus, overcoming limitations current single biotic solutions.

Language: Английский

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The proteome is a terminal electron acceptor

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 1, 2024

Abstract Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. E. coli , for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation respiration. To understand the limits evolutionary consequences metabolic flexibility, we developed a mathematical model coupling chemistry with principles cellular resource allocation. Our integrated clarifies key phenomena, including demonstrating that autotrophs slower than heterotrophs because constraints imposed by intracellular production carbon. further indicates improved adapting state nutrients, revealing an unexpected mode evolution where proteins accumulate mutations benefiting organismal balance. One sentence summary adapt their composition physiological timescales ensure

Language: Английский

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Annotation-free prediction of microbial dioxygen utilization

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 16, 2024

Aerobes require dioxygen (O2) to grow; anaerobes do not. But nearly all microbes — aerobes, anaerobes, and facultative organisms alike express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying assess which are aerobic from genomic data alone. can be overcome by noting that O2 utilization has wide-ranging effects on microbes: aerobes typically have larger genomes, encode more O2-utilizing enzymes, tend use different amino acids in their proteins. Here we show these permit high-quality prediction of genome sequences, with several models displaying >70% balanced accuracy ternary classification task wherein blind guessing is 33.3% accurate. Since annotation compute-intensive relies many assumptions, asked annotation-free methods also perform well. We discovered simple efficient based entirely sequence content e.g. triplets —perform about as well intensive annotation-based algorithms, enabling the rapid processing global-scale predict physiology. To demonstrate utility physiological predictions estimated prevalence along well-studied gradient Black Sea, finding strong quantitative correspondence between local chemistry (O2:sulfide concentration ratio) composition microbial communities. therefore suggest statistical like ours used estimate, or “sense,” pivotal features environment DNA sequencing data.

Language: Английский

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Redox controls on anaerobic ammonium oxidation coupled to reduction of natural organic matter in paddy ecosystems

Biology and Fertility of Soils, Journal Year: 2023, Volume and Issue: 59(8), P. 863 - 871

Published: Aug. 7, 2023

Language: Английский

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chem16S: community-level chemical metrics for exploring genomic adaptation to environments

Bioinformatics, Journal Year: 2023, Volume and Issue: 39(9)

Published: Sept. 1, 2023

The chem16S package combines taxonomic classifications of 16S rRNA gene sequences with amino acid compositions prokaryotic reference proteomes to generate community proteomes. Taxonomic from the RDP Classifier or data objects created by phyloseq R are supported. Users can calculate and visualize a variety chemical metrics in order explore effects redox, salinity, other physicochemical variables on genomic adaptation protein at level.Development is hosted https://github.com/jedick/chem16S. Version 1.0.0 freely available Comprehensive Archive Network (CRAN) https://cran.r-project.org/package=chem16S.

Language: Английский

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Annotation-free prediction of microbial dioxygen utilization

mSystems, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 4, 2024

ABSTRACT Aerobes require dioxygen (O 2 ) to grow; anaerobes do not. However, nearly all microbes—aerobes, anaerobes, and facultative organisms alike—express enzymes whose substrates include O , if only for detoxification. This presents a challenge when trying assess which are aerobic from genomic data alone. can be overcome by noting that utilization has wide-ranging effects on microbes: aerobes typically have larger genomes encoding distinctive -utilizing enzymes, example. These permit high-quality prediction of annotated genome sequences, with several models displaying ≈80% accuracy ternary classification task blind guessing is 33% accurate. Since annotation compute-intensive relies many assumptions, we asked annotation-free methods also perform well. We discovered simple efficient based entirely sequence content—e.g., triplets amino acids—perform as well intensive annotation-based classifiers, enabling rapid processing genomes. further show acid trimers useful because they encode information about protein composition phylogeny. To showcase the utility prediction, estimated prevalence in diverse natural environments cataloged Earth Microbiome Project. Focusing well-studied gradient Black Sea, found quantitative correspondence between local chemistry :sulfide concentration ratio) microbial communities. We, therefore, suggest statistical like ours might used estimate, or “sense,” pivotal features chemical environment using DNA sequencing data. IMPORTANCE now access wide variety environments. document bewildering diversity microbes, known their Physiology—an organism’s capacity engage metabolically its environment—may provide more lens than taxonomy understanding As an example this broader principle, developed algorithms accurately predict directly sequences without annotating genes, e.g., considering acids sequences. Annotation-free enable characterization samples, highlighting levels set Sea. suggests repurposed multi-pronged sensor, estimating concentrations other key facets complex settings.

Language: Английский

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Redox Gradient Shapes the Chemical Composition of Peatland Microbial Communities

Geobiology, Journal Year: 2024, Volume and Issue: 22(6)

Published: Oct. 30, 2024

ABSTRACT The response of soil carbon to climate change and anthropogenic forcing depends on the relationship between physicochemical variables environment microbial communities. In anoxic soils that store large amounts organic carbon, it can be hypothesized low amount catabolic energy available leads organisms minimize costs biosynthesis, which may shape composition To test this hypothesis, thermodynamic modeling was used assess link redox gradients in ombrotrophic peatland Marcell Experimental Forest (Minnesota, USA) chemical taxonomic average amino acid community‐level proteins, called hereafter model calculated from shotgun metagenomic sequencing. oxidation state proteins decreases linearly −0.14 at 10 cm depth −0.17 150 depth. Calculating equilibrium activities for a wide range conditions allows identification potential maximum activity. Consistent with measurements across peat soils, Eh logarithmically an value 300 mV depth, close stability domain goethite relative Fe 2+ , −200 cm, within CH 4 CO 2 . correlation identified abundance enables predicting evolution as function Eh. is consistent measured gene abundance, evolves aerobic bacteria surface including Acidobacteria, Proteobacteria, Verrumicrobia, anaerobes dominated by Crenarchaeota. These results indicate imposed gradient shapes both By providing mechanistic understanding community environmental conditions, work sheds new light mechanisms govern life opens up prospects geochemical changing environments.

Language: Английский

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Coexistence of anodic and cathodic reactions at the scale of a single microbial electrode elucidated by coupling experimental, analytical and numerical approaches

Journal of Power Sources, Journal Year: 2024, Volume and Issue: 624, P. 235600 - 235600

Published: Oct. 17, 2024

Language: Английский

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