Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria

Köstlbacher, Stephan; Collingro, Astrid; Halter, Tamara; Domman, Daryl; Horn, Matthias

doi:10.1016/j.cub.2020.10.030

Cited by 26 publications

(23 citation statements)

References 129 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some environmental chlamydiae encode features that deviate from the generally highly conserved biology of the majority of known chlamydiae. Among these are gene sets for a flagellar apparatus and a chemosensing system 15 , 18 , 19 , 51 , 52 , a conjugative type IV secretion system 15 , 53 , and the CRISPR-Cas phage defense system 54 , 55 . We recovered all of these features in our extended genome dataset and found support for a more widespread occurrence among different chlamydial lineages (Fig.…”

Section: Resultsmentioning

confidence: 99%

Pangenomics reveals alternative environmental lifestyles among chlamydiae

et al. 2021

Self Cite

View full text Add to dashboard Cite

Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

show abstract

Section: Resultsmentioning

confidence: 99%

Pangenomics reveals alternative environmental lifestyles among chlamydiae

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Plasmid genomes are extremely plastic (38). Accessory genes vary in their presence or absent from the plasmids, which makes plasmid host prediction a complicated task.…”

Section: Machine Learningmentioning

confidence: 99%

“…Some of the other false positives might potentially be new discoveries relating to plasmid transmission in diverse hosts, although this theory should be validated experimentally. (38). Accessory genes vary in their presence or absent from the plasmids, which makes plasmid host prediction a complicated task.…”

Section: Machine Learningmentioning

confidence: 99%

PlasmidHostFinder: Prediction of plasmid hosts using random forest

Aytan-Aktug

Clausen

Szarvas

et al. 2021

Preprint

View full text Add to dashboard Cite

Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods, compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids based on the random forest machine learning method. We trained the models with 8,519 plasmids from 359 different bacterial species per taxonomic level, where the models achieved 0.662 and 0.867 Matthews correlation coefficients at the species and order levels, respectively. Our results suggest that despite the diverse nature and genetic plasticity of plasmids, our random forest model can accurately distinguish between plasmid hosts. This tool can be used online through Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/PlasmidHostFinder/).

show abstract

“…> $ % !" < $ % in our data set, pathogenicity is a key aspect of bacterial lifestyle that has been suggested to be important for plasmid gene content, such as antibiotic resistance and virulence factors 6,40,52,53 .…”

Section: Broad Host-range Pathogens Are Most Likely To Carry Genes Fomentioning

confidence: 99%

“…Plasmids of broad host-range pathogens carry many pathogenicity genes. We suspected that the additional extracellular proteins coded for by plasmids of broad host-range species, compared to narrow host-range species, may be particularly involved in facilitating pathogenicity 40,52,53 . To investigate this, we used the program MP3 54 to assign a each extracellular protein as either 'pathogenic' or 'non-pathogenic'.…”

Section: No Invasionmentioning

confidence: 99%

Plasmids facilitate pathogenicity, not cooperation, in bacteria

Dewar

Thomas

Scott

et al. 2021

Preprint

View full text Add to dashboard Cite

Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from both theoretical and genomic analyses. In contrast, with a comparative analysis across 51 diverse species, we found that genes for extracellular proteins, which are likely to act as cooperative ‘public goods’, were not more likely to be carried on either: (i) plasmids compared to chromosomes; or (ii) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that while horizontal gene transfer can help cooperative genes initially invade a population, it does not favour the longer-term maintenance of cooperation. Instead, we found that genes for extracellular proteins were more likely to be on plasmids when they coded for pathogenic virulence traits, in pathogenic bacteria with a broad host-range. Taken together, these results support an alternate hypothesis, that plasmid gene location confers benefits other than horizontal gene transfer.

show abstract

Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria

Cited by 26 publications

References 129 publications

Pangenomics reveals alternative environmental lifestyles among chlamydiae

Pangenomics reveals alternative environmental lifestyles among chlamydiae

PlasmidHostFinder: Prediction of plasmid hosts using random forest

Plasmids facilitate pathogenicity, not cooperation, in bacteria

Contact Info

Product

Resources

About