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1. Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp.

   https://doi.org/10.3389/ffunb.2023.1285531  

   Cailleau, Guillaume ; Hanson, Buck T. ; Cravero, Melissa ; Zhioua, Sami ; Hilpish, Patrick ; Ruiz, Celia ; Robinson, Aaron J. ; Kelliher, Julia M. ; Morales, Demosthenes ; Gallegos-Graves, La Verne ; et al ( December 2023 , Frontiers in Fungal Biology)

   Members of the fungal genusMorchellaare widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained fromMorchellaisolates grownin vitro. These investigations included diverse representatives from both Elata and EsculentaMorchellaclades. Unique bacterial community compositions were observed across the various structures examined, both within and across individualMorchellaisolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genusPseudomonasandRalstoniaconstituted the core bacterial associates ofMorchellamycelia and sclerotia, while other genera (e.g.,Pedobacterspp.,Deviosaspp., andBradyrhizobiumspp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance ofPseudomonasas a key member of the bacteriome was supported by the isolation of severalPseudomonasstrains from mycelia duringin vitrocultivation. Four of the six mycelial-derivedPseudomonasisolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and variousMorchellaisolates. Genome sequences obtained from thesePseudomonasisolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence thatPseudomonasspp. are frequently associated withMorchellaand these associations may greatly impact fungal physiology.

    

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2. The specificity of Burkholderia symbionts in the social amoeba farming symbiosis: Prevalence, species, genetic and phenotypic diversity

   https://doi.org/10.1111/mec.14982  

   Haselkorn, Tamara S. ; DiSalvo, Susanne ; Miller, Jacob W. ; Bashir, Usman ; Brock, Debra A. ; Queller, David C. ; Strassmann, Joan E. ( February 2019 , Molecular Ecology)

   The establishment of symbioses between eukaryotic hosts and bacterial symbionts in nature is a dynamic process. The formation of such relationships depends on the life history of both partners. Bacterial symbionts of amoebae may have unique evolutionary trajectories to the symbiont lifestyle, because bacteria are typically ingested as prey. To persist after ingestion, bacteria must first survive phagocytosis. In the social amoebaDictyostelium discoideum, certain strains ofBurkholderiabacteria are able to resist amoebal digestion and maintain a persistent relationship that includes carriage throughout the amoeba's social cycle that culminates in spore formation. SomeBurkholderiastrains allow their host to carry other bacteria, as food. This carried food is released in new environments in a trait called farming. To better understand the diversity and prevalence ofBurkholderiasymbionts and the traits they impart to their amoebae hosts, we first screened 700 natural isolates ofD. discoideumand found 25% infected withBurkholderia. We next used a multilocus phylogenetic analysis and identified two independent transitions byBurkholderiato the symbiotic lifestyle. Finally, we tested the ability of 38 strains ofBurkholderiafromD. discoideum, as well as strains isolated from other sources, for traits relevant to symbiosis inD. discoideum. OnlyD. discoideumnative isolates belonging to theBurkholderia agricolaris,B. hayleyella, andB. bonnieaspecies were able to form persistent symbiotic associations withD. discoideum.TheBurkholderia–Dictyosteliumrelationship provides a promising arena for further studies of the pathway to symbiosis in a unique system.

    

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3. Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development

   https://doi.org/10.1002/ece3.5924  

   Noh, Suegene ; Christopher, Lauren ; Strassmann, Joan E. ; Queller, David C. ( January 2020 , Ecology and Evolution)

   When multiple strains of microbes form social groups, such as the multicellular fruiting bodies ofDictyostelium discoideum, conflict can arise regarding cell fate. Both fixed and plastic differences among strains can contribute to cell fate, and plastic responses may be particularly important if social environments frequently change. We used RNA‐sequencing and photographic time series analysis to detect possible conflict‐induced plastic differences between wildD.discoideumaggregates formed by single strains compared with mixed pairs of strains (chimeras). We found one hundred and two differentially expressed genes that were enriched for biological processes including cytoskeleton organization and cyclic AMP response (up‐regulated in chimeras), and DNA replication and cell cycle (down‐regulated in chimeras). In addition, our data indicate that in reference to a time series of multicellular development in the laboratory strain AX4, chimeras may be slightly behind clonal aggregates in their development. Finally, phenotypic analysis supported slower splitting of aggregates and a nonsignificant trend for larger group sizes in chimeras. The transcriptomic comparison and phenotypic analyses support discoordination among aggregate group members due to social conflict. These results are consistent with previously observed factors that affect cell fate decision inD.discoideumand provide evidence for plasticity in cAMP signaling and phenotypic coordination during development in response to social conflict inD.discoideumand similar microbial social groups.

    

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4. Multispecies activity screening of microcin J25 mutants yields antimicrobials with increased specificity toward pathogenic Salmonella species relative to human commensal Escherichia coli

   https://doi.org/10.1002/bit.26772  

   Ritter, Seth C. ; Yang, Mike L. ; Kaznessis, Yiannis N. ; Hackel, Benjamin J. ( July 2018 , Biotechnology and Bioengineering)

   Modern large‐scale agricultural practices that incorporate high density farming with subtherapeutic antibiotic dosing are considered a major contributor to the rise of antibiotic‐resistant bacterial infections of humans with species ofSalmonellabeing a leading agriculture‐based bacterial infection. Microcin J25, a potent and highly stable antimicrobial peptide active against Enterobacteriaceae, is a candidate antimicrobial against multipleSalmonellaspecies. Emerging evidence supports the hypothesis that the composition of the microbiota of the gastrointestinal tract prevents a variety of diseases by preventing infectious agents from proliferating. Reducing clearance of off‐target bacteria may decrease susceptibility to secondary infection. Of the Enterobacteriaceae susceptible to microcin J25,Escherichia coliare the most abundant within the human gut. To explore the modulation of specificity, a collection of 207 mutants encompassing 12 positions in both the ring and loop of microcin J25 was built and tested for activity againstSalmonellaandE. colistrains. As has been found previously, mutational tolerance of ring residues was lower than loop residues, with 22% and 51% of mutations, respectively, retaining activity toward at least one target within the target organism test panel. The multitarget screening elucidated increased mutational tolerance at position G2, G3, and G14 than previously identified in panels composed of single targets. Multiple mutations conferred differential response between the different targets. Examination of specificity differences between mutants found that 30% showed significant improvements to specificity toward any of the targets. Generation and testing of a combinatorial library designed from the point‐mutant study revealed that microcin J25^I13Treduces off‐target activity toward commensal human‐derivedE. coliisolates by 81% relative toSalmonella entericaserovar Enteritidis. These in vitro specificity improvements are likely to improve in vivo treatment efficacy by reducing clearance of commensal bacteria in the gastrointestinal tract of hosts.

    

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5. Population structure of bla KPC-harbouring IncN plasmids at a New York City medical centre and evidence for multi-species horizontal transmission

   https://doi.org/10.1093/jac/dkac114  

   Gomez-Simmonds, Angela ; Annavajhala, Medini K. ; Tang, Nina ; Rozenberg, Felix D. ; Ahmad, Mehrose ; Park, Heekuk ; Lopatkin, Allison J. ; Uhlemann, Anne Catrin ( April 2022 , Journal of Antimicrobial Chemotherapy)

   Carbapenem-resistant Enterobacterales (CRE) are highly concerning MDR pathogens. Horizontal transfer of broad-host-range IncN plasmids may contribute to the dissemination of the Klebsiella pneumoniae carbapenemase (KPC), spreading carbapenem resistance among unrelated bacteria. However, the population structure and genetic diversity of IncN plasmids has not been fully elucidated.

   We reconstructed blaKPC-harbouring IncN plasmid genomes to characterize shared gene content, structural variability, and putative horizontal transfer within and across patients and diverse bacterial clones.

   We performed short- and long-read sequencing and hybrid assembly on 45 CRE isolates with blaKPC-harbouring IncN plasmids. Eight serial isolates from two patients were included to assess intra-patient plasmid dynamics. Comparative genomic analysis was performed to assess structural and sequence similarity across plasmids. Within IncN sublineages defined by plasmid MLST and kmer-based clustering, phylogenetic analysis was used to identify closely related plasmids.

   Comparative analysis of IncN plasmid genomes revealed substantial heterogeneity including large rearrangements in serial patient plasmids and differences in structure and content across plasmid clusters. Within plasmid sublineages, core genome content and resistance gene regions were largely conserved. Closely related plasmids (≤1 SNP) were found in highly diverse isolates, including ten pST6 plasmids found in eight bacterial clones from three different species.

   Genomic analysis of blaKPC-harbouring IncN plasmids revealed the presence of several distinct sublineages as well as substantial host diversity within plasmid clusters suggestive of frequent mobilization. This study reveals complex plasmid dynamics within a single plasmid family, highlighting the challenge of tracking plasmid-mediated transmission of blaKPC in clinical settings.

    

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