Population genomics of Klebsiella pneumoniae

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(6), P. 344 - 359

Published: Feb. 13, 2020

Language: Английский

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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(3), P. e1007732 - e1007732

Published: March 19, 2020

The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms occurrence a given species. These usually lack multivariate statistical models infer the partitions optimal number classes don't account genome organization. We introduce graph structure model pangenomes which nodes represent edges genomic neighborhood. Our method, named PPanGGOLiN, using an Expectation-Maximization algorithm based on Bernoulli Mixture Model coupled with Markov Random Field. This approach takes into topology presence/absence genes persistent, cloud, one or several shell partitions. By analyzing partitioned pangenome graphs isolate genomes from 439 species metagenome-assembled 78 species, we demonstrate that our method is effective estimating persistent genome. Interestingly, it shows key element understand dynamics, presumably because reflects how present at intermediate frequencies drive adaptation its proportion independent size. graph-based proposed by PPanGGOLiN useful depict overall diversity thousands strains compact provides basis very large scale genomics. software freely available https://github.com/labgem/PPanGGOLiN.

Language: Английский

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The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution

Trends in Microbiology, Journal Year: 2020, Volume and Issue: 29(1), P. 8 - 18

Published: June 11, 2020

Language: Английский

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Plant NLR diversity: the known unknowns of pan-NLRomes

The Plant Cell, Journal Year: 2021, Volume and Issue: 33(4), P. 814 - 831

Published: Jan. 1, 2021

Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, especially intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family in same genome, between individuals species. While this diversity has long been appreciated, its true extent remained unknown. With pan-genome pan-NLRome studies becoming more comprehensive, our knowledge NLR sequence is growing rapidly, pan-NLRomes provide powerful platforms for assigning function NLRs. These efforts an important step toward goal comprehensively predicting from alone whether provides disease resistance, if so, which pathogens.

Language: Английский

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Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1861)

Published: Aug. 22, 2022

Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those their hosts. In general, costly to donor cell while potentially beneficial recipients. The diversity and plasticity cell-MGEs interactions, among MGEs, result in complex evolutionary processes where source, or even existence selection for maintaining a function genome, unclear. For example, MGE-driven HGT depends on envelope structures defense systems, many these transferred by MGEs themselves. can spur periods intense increasing own rates horizontal transmission upon communicating, eavesdropping, sensing environment host physiology. This may high-frequency genes unrelated MGE. Here, we review how drive mechanisms, selective pressures genomic traits affect flow, therefore adaptation, populations. encoding adaptive niche-defining means that intragenomic conflicts alliances between cells key functional diversification. article part discussion meeting issue 'Genomic population pathogens'.

Language: Английский

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Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 50(6), P. 3155 - 3168

Published: March 11, 2022

Abstract Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution the dispersal of cargo functions like antibiotic resistance. However, each these MGE types is usually annotated analysed individually, hampering a global understanding phylogenetic environmental patterns dispersal. We thus developed computational framework that captures diverse types, their cargos MGE-mediated horizontal transfer events, using recombinases ubiquitous marker genes pangenome information for boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific six operational which together contain on average 13% all genome. Transposable elements (TEs) dominated across taxa (∼1.7 occurrences), outnumbering phage-like (<0.4 million). recorded numerous events phyla habitats involving disentangled quantified extent hitchhiking TEs (17%) integrons (63%) other categories, established dominant carriers resistance genes. integrated findings into resource (proMGE.embl.de), should facilitate future studies large mobile part its

Language: Английский

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A host of armor: Prokaryotic immune strategies against mobile genetic elements

Cell Reports, Journal Year: 2023, Volume and Issue: 42(7), P. 112672 - 112672

Published: June 21, 2023

Prokaryotic adaptation is strongly influenced by the horizontal acquisition of beneficial traits via mobile genetic elements (MGEs), such as viruses/bacteriophages and plasmids. However, MGEs can also impose a fitness cost due to their often parasitic nature differing evolutionary trajectories. In response, prokaryotes have evolved diverse immune mechanisms against MGEs. Recently, our understanding abundance diversity prokaryotic systems has greatly expanded. These defense degrade invading material, inhibit genome replication, or trigger abortive infection, leading population protection. this review, we highlight these strategies, focusing on most recent discoveries. The study defenses not only sheds light microbial evolution but uncovers novel enzymatic activities with promising biotechnological applications.

Language: Английский

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A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 11, 2023

Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct large-scale excavation soil matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 metagenomes. We identify 16,530 21,077 species-level (SGBs) unknown SGBs (uSGBs), which expand archaeal bacterial diversity across the tree life. also illustrate pivotal role uSGBs in augmenting microbiome’s functional landscape intra-species diversity, providing large proportions 43,169 biosynthetic gene clusters 8545 CRISPR-Cas genes. Additionally, determine that contributed 84.6% previously unexplored viral-host associations catalogue. The catalogue provides useful genomic resource for further studies investigating resources.

Language: Английский

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Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals

Genes, Journal Year: 2023, Volume and Issue: 14(7), P. 1484 - 1484

Published: July 21, 2023

Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The is posing increased demand for food, thereby pushing an acceleration in agricultural production. Furthermore, anthropogenic activities have resulted environmental pollution such as water soil degradation well alterations the composition concentration of gases. These affecting not only biodiversity loss but also physio-biochemical processes crop plants, resulting a stress-induced decline yield. To overcome problems ensure supply food material, consistent efforts being made develop strategies techniques increase yield enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication initially remained dependent on phenotype-based selection improvement. But it has grown through cytological biochemical methods, newer contemporary methods based DNA-marker-based help agronomically useful traits. now supported by high-end molecular biology tools like PCR, high-throughput genotyping phenotyping, data from morpho-physiology, statistical tools, bioinformatics, machine learning. After establishing its worth animal breeding, genomic (GS), improved variant marker-assisted (MAS), way into crop-breeding programs powerful tool. novel innovative marker-based models genetic evaluation, GS makes use markers. can amend complex traits shorten period, making advantageous over pedigree (MAS). It reduces time resources required plant while allowing gain attributes. been taken new heights integrating advanced technologies speed learning, environmental/weather further harness potential, approach known integrated (IGS). This review highlights IGS strategies, procedures, approaches, associated emerging issues, with special emphasis cereal crops. In this domain, highlight potential cutting-edge innovation climate-smart crops endure abiotic stresses motive keeping production quality at par global demand.

Language: Английский

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Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiology and Molecular Biology Reviews, Journal Year: 2023, Volume and Issue: 87(3)

Published: June 27, 2023

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, water filtration. are also intimately associated with complex multicellular organisms such as humans, other animals, plants, insects perform crucial the health of their hosts. Although we starting to understand microbiomes in different systems interconnected, there is still a poor understanding microbiome transfer connectivity. In this review show how connected within transferred between habitats discuss functional consequences these connections. Microbiome occurs abiotic (e.g., air, soil, water) biotic environments, can either be mediated through vectors or food) direct interactions. Such processes may include transmission pathogens antibiotic resistance genes. However, here, highlight fact positive effects on human where transmitted microorganisms potentially providing novel adaptation ecosystems.

Language: Английский

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