18 Result(s)
within
Kiran Raosaheb Patil
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Article
High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities
The human gut microbiome is a key contributor to health, and its perturbations are linked to many diseases. Small-molecule xenobiotics such as drugs, chemical pollutants and food additives can alter the microb...
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Article
Metabolic exchanges are ubiquitous in natural microbial communities
Microbial communities drive global biogeochemical cycles and shape the health of plants and animals—including humans. Their structure and function are determined by ecological and environmental interactions th...
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Article
Open AccessCo-translational assembly orchestrates competing biogenesis pathways
During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to produc...
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Article
Unravelling the collateral damage of antibiotics on gut bacteria
Antibiotics are used to fight pathogens but also target commensal bacteria, disturbing the composition of gut microbiota and causing dysbiosis and disease1. Despite this well-known collateral damage, the activity...
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Article
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studie...
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Chapter
Yeast Genome-Scale Metabolic Models for Simulating Genotype–Phenotype Relations
Understanding genotype–phenotype dependency is a universal aim for all life sciences. While the complete genotype–phenotype relations remain challenging to resolve, metabolic phenotypes are moving within the r...
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Article
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host–microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth charac...
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Article
Extensive impact of non-antibiotic drugs on human gut bacteria
A few commonly used non-antibiotic drugs have recently been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Here, we screened more than 1,000 marketed drugs...
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Article
Towards standards for human fecal sample processing in metagenomic studies
Testing 21 different fecal DNA extraction protocols in multiple laboratories results in a standardized protocol with the potential to improve comparability across human gut microbiome studies.
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Article
Open AccessYeast metabolic chassis designs for diverse biotechnological products
The diversity of industrially important molecules for which microbial production routes have been experimentally demonstrated is rapidly increasing. The development of economically viable producer cells is, ho...
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Article
The metabolic background is a global player in Saccharomyces gene expression epistasis
The regulation of gene expression in response to nutrient availability is fundamental to the genotype–phenotype relationship. The metabolic–genetic make-up of the cell, as reflected in auxotrophy, is hence lik...
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Protocol
Model-Guided Identification of Gene Deletion Targets for Metabolic Engineering in Saccharomyces cerevisiae
Identification of metabolic engineering strategies for rerouting intracellular fluxes towards a desired product is often a challenging task owing to the topological and regulatory complexity of metabolic netwo...
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Article
Open AccessReconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
Synechocystis sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform - an attractive cell factory capable of using CO2 and light as carbon and energy source, respectively. ...
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Article
Open AccessImproved vanillin production in baker's yeast through in silico design
Vanillin is one of the most widely used flavouring agents, originally obtained from cured seed pods of the vanilla orchid Vanilla planifolia. Currently vanillin is mostly produced via chemical synthesis. A de nov...
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Article
Open AccessNatural computation meta-heuristics for the in silico optimization of microbial strains
One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metab...
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Article
Open AccessArchitecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-...
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Article
Open AccessEvolutionary programming as a platform for in silico metabolic engineering
Through genetic engineering it is possible to introduce targeted genetic changes and hereby engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, owing to the c...
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Article
The role of high-throughput transcriptome analysis in metabolic engineering
The phenotypic response of a cell results from a well orchestrated web of complex interactions which propagate from the genetic architecture through the metabolic flux network. To rationally design cell factor...
