Publications by authors named "Christopher M Field"

In contrast to the large body of work on bioactive natural products from individually cultivated bacteria, the chemistry of environmental microbial communities remains largely elusive. Here, we present a comprehensive bioinformatic and functional study on a complex and interaction-rich ecosystem, algal-bacterial (microbial) mats of Lake Chilika in India, Asia's largest brackish water body. We report the bacterial compositional dynamics over the mat life cycle, >1,300 reconstructed environmental genomes harboring >2,200 biosynthetic gene clusters (BGCs), the successful cultivation of a widespread core microbiome member belonging to the genus , heterologous reconstitution of two silent biosynthetic pathways, and new compounds with potent protease inhibitory and antiviral activities.

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Endosymbioses have profoundly impacted the evolution of life and continue to shape the ecology of a wide range of species. They give rise to new combinations of biochemical capabilities that promote innovation and diversification. Despite the many examples of known endosymbioses across the tree of life, their de novo emergence is rare and challenging to uncover in retrospect.

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Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration.

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Motivation: DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills.

Results: Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups.

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Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria.

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In recent years, a variety of fungal cyclic peptides with interesting bioactivities have been discovered. For many of these peptides, the biosynthetic pathways are unknown and their elucidation often holds surprises. The cyclic and backbone N-methylated omphalotins from Omphalotus olearius were recently shown to constitute a novel class (borosins) of ribosomally synthesized and posttranslationally modified peptides, members of which are produced by many fungi, including species of the genus Rhizopogon.

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The plant microbiota consists of a multitude of microorganisms that can affect plant health and fitness. However, it is currently unclear how the plant shapes its leaf microbiota and what role the plant immune system plays in this process. Here, we evaluated Arabidopsis thaliana mutants with defects in different parts of the immune system for an altered bacterial community assembly using a gnotobiotic system.

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Plants, like other multicellular lifeforms, are colonized by microorganisms. How plants respond to their microbiota is currently not well understood. We used a phylogenetically diverse set of 39 endogenous bacterial strains from Arabidopsis thaliana leaves to assess host transcriptional and metabolic adaptations to bacterial encounters.

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Background: Temperate phages influence the density, diversity and function of bacterial populations. Historically, they have been described as carriers of toxins. More recently, they have also been recognised as direct modulators of the gut microbiome, and indirectly of host health and disease.

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Backbone N-methylation and macrocyclization improve the pharmacological properties of peptides by enhancing their proteolytic stability, membrane permeability and target selectivity. Borosins are backbone N-methylated peptide macrocycles derived from a precursor protein which contains a peptide α-N-methyltransferase domain autocatalytically modifying the core peptide located at its C-terminus. Founding members of borosins are the omphalotins from the mushroom Omphalotus olearius (omphalotins A-I) with nine out of 12 L-amino acids being backbone N-methylated.

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Bacterial specialized metabolites are increasingly recognized as important factors in animal-microbiome interactions: for example, by providing the host with chemical defenses. Even in chemically rich animals, such compounds have been found to originate from individual members of more diverse microbiomes. Here, we identified a remarkable case of a moderately complex microbiome in the sponge host in which multiple symbionts jointly generate chemical diversity.

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Article Synopsis
  • Ocean microbial communities play a crucial role in influencing the planet's biogeochemistry, food webs, and climate, yet there's limited understanding of their global transcriptome variations.
  • A comprehensive dataset of 187 metatranscriptomes and 370 metagenomes collected from 126 sampling stations worldwide has been established, highlighting 47 million genes for studying community-level transcriptomes across different ocean depths.
  • The study reveals that gene expression changes impacting community transcriptomes vary with environmental conditions, notably finding lower gene expression contributions in polar regions, suggesting that community composition may be more affected by ocean warming than gene regulation.
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Multicellular organisms, including plants, are colonized by microorganisms, some of which are beneficial to growth and health. The assembly rules for establishing plant microbiota are not well understood, and neither is the extent to which their members interact. We conducted drop-out and late introduction experiments by inoculating Arabidopsis thaliana with synthetic communities from a resource of 62 native bacterial strains to test how arrival order shapes community structure.

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Article Synopsis
  • - The General Stress Response (GSR) in alphaproteobacteria, controlled by the sigma factor EcfG, helps the bacteria survive various stressors by regulating multiple stress-resistant genes.
  • - Transcriptome analyses of Sphingomonas melonis Fr1 revealed that EcfG not only regulates stress response proteins but also fine-tunes them through novel regulators like NepR2.
  • - The study found that GSR is connected to the regulation of motility and biofilm formation, indicating a complex system in S. melonis Fr1 that enhances resilience and optimizes resource use in challenging environments.
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Indole is a bacterial signalling molecule that blocks E. coli cell division at concentrations of 3-5 mM. We have shown that indole is a proton ionophore and that this activity is key to the inhibition of division.

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In the absence of active partitioning, strict control of plasmid copy number is required to minimise the possibility of plasmid loss at bacterial cell division. An important cause of multicopy plasmid instability is the formation of plasmid dimers by recombination and their subsequent proliferation by over-replication in a process known as the dimer catastrophe. This leads to the formation of dimer-only cells in which plasmid copy number is substantially lower than in cells containing only monomers, and which have a greatly increased probability of plasmid loss at division.

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