Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss)

Diverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. We hypothesized that fecal samples representing the gut microbiota of rainbow trout could be associated with differential growth rates observed in fish breeding programs. If true, harnessing the functionality of this microbiota can improve the profitability of aquaculture. The first objective of this study was to test this hypothesis if gut microbiota is associated with fish growth rate (body weight). Four full-sibling families were stocked in the same tank and fed an identical diet. Two fast-growing and two slow-growing fish were selected from each family for 16S rRNA microbiota profiling.https://doi.org/10.1186/s12864-019-6175-

Contribution of the a-baumannii A1S_0114 gene to the interaction with eukaryotic cells and virulence

Genetic and functional studies showed that some components of the Acinetobacter baumannii ATCC 17978 A1S_0112-A1S_0119 gene cluster are critical for biofilm biogenesis and surface motility. Recently, our group has shown that the A1S_0114 gene was involved in biofilm formation, a process related with pathogenesis. Confirming our previous results, microscopy images revealed that the ATCC 17978 10114 derivative lacking this gene was unable to form a mature biofilm structure. Therefore, other bacterial phenotypes were analyzed to determine the role of this gene in the pathogenicity of A. baumannii ATCC 17978. The interaction of the ATCC 17978 parental strain and the 10114 mutant with A549 human alveolar epithelial cells was quantified revealing that the A1S_0114 gene was necessary for proper attachment to A549 cells. This dependency correlates with the negative effect of the A1S_0114 deletion on the expression of genes coding for surface proteins and pili-assembly systems, which are known to play a role in adhesion. Three different experimental animal models, including vertebrate and invertebrate hosts, confirmed the role of the A1S_0114 gene in virulence. All of the experimental infection assays indicated that the virulence of the ATCC 17978 was significantly reduced when this gene was inactivated. Finally, we discovered that the A1S_0114 gene was involved in the production of a small lipopeptide-like compound herein referred to as acinetin 505 (Ac-505). Ac-505 was isolated from ATCC 17978 spent media and its chemical structure was interpreted by mass spectrometry. Overall, our observations provide novel information on the role of the A1S_0114 gene in A. baumannii’s pathobiology and lay the foundation for future work to determine the mechanisms by which Ac-505, or possibly an Ac-505 precursor, could execute critical functions as a secondary metaboliteS

Two Acinetobacter baumannii Isolates Obtained From a Fatal Necrotizing Fasciitis Infection Display Distinct Genomic and Phenotypic Characteristics in Comparison to Type Strains

Acinetobacter baumannii has been recognized as a critical pathogen that causes severe infections worldwide not only because of the emergence of extensively drug-resistant (XDR) derivatives, but also because of its ability to persist in medical environments and colonize compromised patients. While there are numerous reports describing the mechanisms by which this pathogen acquires resistance genes, little is known regarding A. baumannii's virulence functions associated with rare manifestations of infection such as necrotizing fasciitis, making the determination and implementation of alternative therapeutic targets problematic. To address this knowledge gap, this report describes the analysis of the NFAb-1 and NFAb-2 XDR isolates, which were obtained at two time points during a fatal case of necrotizing fasciitis, at the genomic and functional levels. The comparative genomic analysis of these isolates with the ATCC 19606T and ATCC 17978 strains showed that the NFAb-1 and NFAb-2 isolates are genetically different from each other as well as different from the ATCC 19606T and ATCC 17978 clinical isolates. These genomic differences could be reflected in phenotypic differences observed in these NFAb isolates. Biofilm, cell viability and flow cytometry assays indicate that all tested strains caused significant decreases in A549 human alveolar epithelial cell viability with ATCC 17978, NFAb-1 and NFAb-2 producing significantly less biofilm and significantly more hemolysis and capacity for intracellular invasion than ATCC 19606T. NFAb-1 and NFAb-2 also demonstrated negligible surface motility but significant twitching motility compared to ATCC 19606T and ATCC 17978, likely due to the presence of pili exceeding 2 µm in length, which are significantly longer and different from those previously described in the ATCC 19606T and ATCC 17978 strains. Interestingly, infection with cells of the NFAb-1 isolate, which were obtained from a premortem blood sample, lead to significantly higher mortality rates than NFAb-2 bacteria, which were obtained from postmortem tissue samples, when tested using the Galleria mellonella in vivo infection model. These observations suggest potential changes in the virulence phenotype of the A. baumannii necrotizing fasciitis isolates over the course of infection by mechanisms and cell processes that remain to be identified

Virulence of <i>A. baumannii</i> ATCC 19606^T parental and isogenic derivatives.

<p>(A) Persistence of bacteria in the presence of A549 monolayers. Bacteria (10³) we added to 95% confluent monolayer maintained in mHBSS. The resulting CFUs were quantified after 24 h incubation at 37°C in 5% CO₂. (B and C) <i>G. mellonella</i> killing assays. Caterpillars were infected with 1×10⁵ bacteria of the ATCC 19606^T parental strain (19606), or the s1 or 3069 iron-deficient isogenic derivatives in the absence (panel B) or the presence (panel C) of 100 µM Fe₃Cl and incubated at 37°C in darkness. Moth death was determined daily for six days. Caterpillars injected with comparable volumes of PBS or PBS plus 100 µM Fe₃Cl were used as negative controls.</p

Analysis of culture supernatants.

<p>HPLC profiles of sterile succinate medium (medium) or culture supernatants from the ATCC 19606^T parental strain (19606) or the AYE clinical isolate cultured in the absence (AYE) or the presence of 100 µM DHBA (AYE+DHBA).</p

Components of the gene cluster containing the <i>entA-entB</i> genes in different <i>A. baumannii</i> genomes.

a<p>Additional coding regions compared to the ATCC 19606^T gene cluster shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036493#pone-0036493-g001" target="_blank">Fig. 1A</a>.</p>b<p>Numbers should be preceded by the annotation HMPREF0010_ according to the information presented in the <i>A. baumannii</i> Broad Institute genome site.</p>c<p>Not applicable.</p

Iron acquisition phenotype of <i>E. coli</i> enterobactin deficient mutants.

<p>(A) Growth of the <i>E. coli</i> AN193 <i>entA</i> mutant harboring no plasmid or transformed with pMU925, pMU858, pMU968, pMU804 or pMU807 in LB broth in the absence or the presence of 250 µM DIP. (B) Growth of the <i>E. coli</i> AN192 <i>entB</i> mutant harboring no plasmid or transformed with pMU925 or pMU964 in LB broth in the absence or the presence of 250 µM DIP. The plasmids pMU925, pMU968 and pMU804 harbor the <i>entA</i>/<i>entB</i> orthologs cloned from ATCC 19606^T, AYE, and ATCC 17978, respectively. Plasmid pMU858 harbors an insertionally inactivated ATCC 19606^T<i>entA</i> derivative. Plasmid pMU964 harbors the ATCC 19606^T<i>basF</i> gene.</p

Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound.

Every year, more than 250,000 invasive candidiasis infections are reported with 50,000 deaths worldwide. The limited number of antifungal agents necessitates the need for alternative antifungals with potential novel targets. The 2-benzylidenebenzofuran-3-(2H)-ones have become an attractive scaffold for antifungal drug design. This study aimed to determine the antifungal activity of a synthetic aurone compound and characterize its mode of action. Using the broth microdilution method, aurone SH1009 exhibited inhibition against C. albicans, including resistant isolates, as well as C. glabrata, and C. tropicalis with IC50 values of 4-29 μM. Cytotoxicity assays using human THP-1, HepG2, and A549 human cell lines showed selective toxicity toward fungal cells. The mode of action for SH1009 was characterized using chemical-genetic interaction via haploinsufficiency (HIP) and homozygous (HOP) profiling of a uniquely barcoded Saccharomyces cerevisiae mutant collection. Approximately 5300 mutants were competitively treated with SH1009 followed by DNA extraction, amplification of unique barcodes, and quantification of each mutant using multiplexed next-generation sequencing. Barcode post-sequencing analysis revealed 238 sensitive and resistant mutants that significantly (FDR P values ≤ 0.05) responded to aurone SH1009. The enrichment analysis of KEGG pathways and gene ontology demonstrated the cell cycle pathway as the most significantly enriched pathway along with DNA replication, cell division, actin cytoskeleton organization, and endocytosis. Phenotypic studies of these significantly enriched responses were validated in C. albicans. Flow cytometric analysis of SH1009-treated C. albicans revealed a significant accumulation of cells in G1 phase, indicating cell cycle arrest. Fluorescence microscopy detected abnormally interrupted actin dynamics, resulting in enlarged, unbudded cells. RT-qPCR confirmed the effects of SH1009 in differentially expressed cell cycle, actin polymerization, and signal transduction genes. These findings indicate the target of SH1009 as a cell cycle-dependent organization of the actin cytoskeleton, suggesting a novel mode of action of the aurone compound as an antifungal inhibitor