Genetic innovations in animal–microbe symbioses

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 23(1), P. 23 - 39

Published: Aug. 13, 2021

Language: Английский

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Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

The ISME Journal, Journal Year: 2020, Volume and Issue: 14(5), P. 1247 - 1259

Published: Feb. 11, 2020

Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used characterize the strain prokaryotic species. To understand interdependence features (such as number core accessory genes) study impact environmental constraints on evolution conspecific strains, we computed for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes each which respective habitats were assigned. Species habitat ubiquity was associated with several features. In particular, core-genome size more important than genome size. general, preferences had stronger inertia. Environmental explained up 49% variance features, compared 18% by This observation robust when dataset extended 10,100 (59 phyla). importance further accentuated convergent in given type across different clades. For example, soil environment promotes expansion size, while host-associated lead its reduction. Taken together, explored global principles evolution, quantified influence habitat, inertia identified criteria governing specificity.

Language: Английский

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CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa

The ISME Journal, Journal Year: 2020, Volume and Issue: 15(5), P. 1420 - 1433

Published: Dec. 21, 2020

Abstract CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by raises possibility these may constrain horizontal gene transfer. Here we test this hypothesis in opportunistic pathogen Pseudomonas aeruginosa, which has emerged as important model for understanding function. Across diversity P. active are associated smaller genomes higher GC content, suggesting inhibits acquisition Although phage is major target spacers, more than 80% isolates have spacers integrative conjugative elements (ICE) or conserved transfer machinery used plasmids ICE. Consistent results, containing harbour a lower abundance both prophage Crucially, map to ICE integrated into chromosomes closely related lacking immunity. We propose acts constraint transfer, evolutionary mechanisms ensure its maintenance drive loss key ability adapt new niches stressors.

Language: Английский

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Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species

Current Biology, Journal Year: 2020, Volume and Issue: 30(13), P. 2520 - 2531.e7

Published: June 11, 2020

Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little known about the extent which related differ at this level and underlying mechanisms may constrain maintain strain-level diversity. Here, we used shotgun metagenomics characterize compare gut microbiota two honey bee species, Apis mellifera cerana, diverged 6 mya. Although host are colonized largely by same 16S rRNA phylotypes, find that their specific when analyzed genomic resolution. Moreover, despite similar ecology, A. displayed a much higher content compared both per colony individual bee. In particular, repertoire for polysaccharide degradation was massively expanded relative cerana. Bee management practices, divergent ecological adaptation, or habitat size have contributed observed differences these key pollinator species. Our results illustrate closely animal hosts can while displaying levels based on gene. Such likely consequences functioning host-symbiont interactions, highlighting need metagenomic studies understand ecology evolution communities.

Language: Английский

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Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Science Advances, Journal Year: 2021, Volume and Issue: 7(15)

Published: April 9, 2021

The pangenome of Escherichia coli from nearby farms shows how livestock host and local geography shape bacterial populations.

Language: Английский

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Ecogenetics of antibiotic resistance in Listeria monocytogenes

Molecular Microbiology, Journal Year: 2020, Volume and Issue: 113(3), P. 570 - 579

Published: March 1, 2020

Abstract The acquisition process of antibiotic resistance in an otherwise susceptible organism is shaped by the ecology species. Unlike other relevant human pathogens, Listeria monocytogenes has maintained a high rate susceptibility to antibiotics used for decades treat and animal infections. However, L. can acquire genes from organisms’ plasmids conjugative transposons. Ecological factors could account its susceptibility. ubiquitous nature, most frequently including reservoirs unexposed antibiotics, intracellular sanctuaries. remarkably closed genome, reflecting limited community interactions, small population sizes niche specialization. species divided into variants that are specialized specific niches, which reduces possibility coexistence with potential donors resistance. Interactions also hampered interspecies antagonism. occasional increases (and thus acquiring resistance) derive selection based on intrinsic or acquired biocides, heavy metals natural tolerance extreme conditions. High‐quality surveillance emergence key drugs primary therapy mandatory.

Language: Английский

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Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria

Nature Chemistry, Journal Year: 2022, Volume and Issue: 14(6), P. 701 - 712

Published: April 25, 2022

Abstract Microorganisms contribute to the biology and physiology of eukaryotic hosts affect other organisms through natural products. Xenorhabdus Photorhabdus ( XP ) living in mutualistic symbiosis with entomopathogenic nematodes generate products mediate bacteria–nematode–insect interactions. However, a lack systematic analysis biosynthetic gene clusters (BGCs) has limited understanding how interactions between organisms. Here we combine pangenome sequence similarity networks analyse BGCs from 45 strains that cover all sequenced our collection represent almost taxonomy. The identified 1,000 belong 176 families. most conserved families are denoted by 11 BGC classes. We homologously (over)express ubiquitous unique identify compounds featuring unusual architectures. bioactivity evaluation demonstrates prevalent proteasome inhibitors, virulence factors against insects, metallophores insect immunosuppressants. These findings explain functional basis bacterial this tripartite relationship.

Language: Английский

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Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(5)

Published: May 1, 2022

Accessory genes are variably present among members of a species and reservoir adaptive functions. In bacteria, differences in gene distributions individuals largely result from mobile elements that acquire disperse accessory as cargo. contrast, the impact cargo-carrying on eukaryotic evolution remains unknown. Here, we show variation genome content within multiple fungal is facilitated by Starships, newly discovered group massive 110 kb long average, share conserved components, carry diverse arrays genes. We identified hundreds Starship-like regions across every major class filamentous Ascomycetes, including 28 distinct Starships range 27 to 393 last shared common ancestor ca. 400 Ma. Using new long-read assemblies plant pathogen Macrophomina phaseolina, characterize four additional whose activities contribute standing structure content. One these elements, Voyager, inserts into 5S rDNA contains candidate virulence factor increasing copy number has contrasting associations with pathogenic saprophytic growth, suggesting Voyager's activity underlies an ecological trade-off. propose analogs bacterial integrative conjugative based parallels between their components may therefore represent first dedicated agents active transfer eukaryotes. Our results suggest have shaped genomes for millions years reveal concerted route throughout entire phylum.

Language: Английский

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Mechanisms That Shape Microbial Pangenomes

Trends in Microbiology, Journal Year: 2021, Volume and Issue: 29(6), P. 493 - 503

Published: Jan. 9, 2021

Language: Английский

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Current Techniques to Study Beneficial Plant-Microbe Interactions

Microorganisms, Journal Year: 2022, Volume and Issue: 10(7), P. 1380 - 1380

Published: July 8, 2022

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria plants. Some of these methods focus on changes plant others are directed towards assessing physiology biochemistry growth-promoting (PGPB). Here, we provide an overview some current techniques that employed interaction plants with PGPB. These include microbiomes; use DNA genome sequencing understand genes encoded by PGPB; transcriptomics, proteomics, metabolomics PGPB gene expression; editing encapsulation inoculants prior their treat plants; imaging nitrogenase assays; specialized growth chambers for growing monitoring bacterially treated

Language: Английский

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