Arcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness

Metabarcoding for the Monitoring of the Microbiome and Parasitome of Medically Important Mosquito Species in Two Urban and Semi-urban Areas of South Korea

Interactions between microbial communities and the host can modulate mosquito biology, including vector competence. Therefore, future vector biocontrol measures will utilize these interactions and require extensive monitoring of the mosquito microbiome. Metabarcoding strategies will be useful for conducting vector monitoring on a large scale. We used 16S and 18S rRNA gene metabarcoding through iSeq100 sequencing to characterize the microbiome and eukaryome of Aedes albopictus (Skuse 1894) and Culex pipiens (Linnaeus 1758), two globally important vectors present in South Korea. Mosquitoes were collected from an urban and a semi-urban location in South Korea. Bacterial alpha and beta diversities varied by population. Pseudomonadota dominated the microbiomes of both species. The microbiome composition varied by population and was dominated by different taxa. At the genus level, Wolbachia sp. was the most enriched genus in Cx. pipiens, followed by Aeromonas sp. In Ae. Albopictus, the most abundant group was Enterococcus sp. The gregarine parasite Ascogregarina taiwanensis was highly prevalent in Ae. Albopictus and its absence was marked by the presence of seven bacterial taxa. To our knowledge, this is the first characterization of the microbiome of Ae. albopictus and Cx. pipiens in these regions of South Korea and contributes to the current information on the microbiome of mosquito species, which can be used in further studies to assess pathogen-microbiome and microbiome-microbiome interactions.

Depuration of Aliarcobacter butzleri and Malaciobacter molluscorum in Comparison with Escherichia coli in Mussels (Mytilus galloprovincialis) and Oysters (Crassostrea gigas)

Arcobacter-related species are considered emerging food-borne and waterborne pathogens, with shellfish being a suggested reservoir. In a published study that investigated 204 shellfish samples and 476 isolates, the species Arcobacter butzleri (now known as Aliarcobacter butzleri) and Arcobacter molluscorum (now known as Malaciobacter molluscorum) have been isolated as the most dominant species. However, the efficiency of depuration for eliminating A. butzleri and M. molluscorum in comparison with Escherichia coli from mussels and oysters is unknown and is therefore the objective of this investigation. The shellfish depuration process was evaluated in the laboratory, in summer and winter, using mussels and oysters collected from the Ebro Delta harvesting areas after performing a natural contamination and an artificial contamination using the same conditions for both mollusk and seasons. The natural contamination was performed by exposing the shellfish to a freshwater channel that receives untreated sewage from the village of Poble Nou (PNC) and that had a salinity of 10.7-16.8‱. The artificial contamination exposed the shellfish to A. butzleri and E. coli (in one tank) and to M. molluscorum and E. coli in another tank under controlled conditions of salinity (34.5‱) and temperature (20 °C summer and 14 °C winter). When evaluating the reduction in the bacteria load (every 24 h) throughout 120 h, the naturally contaminated shellfish at the PNC showed a higher reduction than the shellfish contaminated at the laboratory, with the exception of M. molluscorum, that at 24 h could not be detected in summer, neither in mussels nor in oysters. This may be attributed to the fact that the bacteria from the PNC were less adapted to the conditions of high salinity (34.5‱) in which the depuration process was performed. Although temperature did not statistically make a difference in depuration, at 20 °C a higher elimination of all bacteria was recorded relative to 14 °C. In general, E. coli survived more in mussels than in oysters, and M. molluscorum suffered in both mollusks a higher reduction than A. butzleri. New studies are required to determine further the safety of bivalves regarding the presence of Arcobacter-related species.

Arcobacteraceae: An Exploration of Antibiotic Resistance Featuring the Latest Research Updates

The Arcobacteraceae bacterial family includes species isolated from animals and related food products. Moreover, these species have been found in other ecological niches, including water. Some species, particularly Arcobacter butzleri and Arcobacter cryaerophilus, have been isolated from human clinical cases and linked to gastrointestinal symptoms. The presence of antibiotic-resistant strains is a concern for public health, considering the possible zoonoses and foodborne infections caused by contaminated food containing bacteria resistant to antibiotic treatments. This review aims to highlight the importance of antibiotic resistance in Arcobacter spp. isolates from several sources, including information about antibiotic classes to which this bacterium has shown resistance. Arcobacter spp. demonstrated a wide spectrum of antibiotic resistance, including several antibiotic resistance genes. Antibiotic resistance genomic traits include efflux pumps and mutations in antibiotic target proteins. The literature shows a high proportion of Arcobacter spp. that are multidrug-resistant. However, studies in the literature have primarily focused on the evaluation of antibiotic resistance in A. butzleri and A. cryaerophilus, as these species are frequently isolated from various sources. These aspects underline the necessity of studies focused on several Arcobacter species that could potentially be isolated from several sources.

Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp

The consumption of contaminated poultry meat is a significant threat for public health, as it implicates in foodborne pathogen infections, such as those caused by Arcobacter. The mitigation of clinical cases requires the understanding of contamination pathways in each food process and the characterization of resident microbiota in the productive environments, so that targeted sanitizing procedures can be effectively implemented. Nowadays these investigations can benefit from the complementary and thoughtful use of culture- and omics-based analyses, although their application in situ is still limited. Therefore, the 16S-rRNA gene-based sequencing of total DNA and the targeted isolation of Arcobacter spp. through enrichment were performed to reconstruct the environmental contamination pathways within a poultry abattoir, as well as the dynamics and distribution of this emerging pathogen. To that scope, broiler's neck skin and caeca have been sampled during processing, while environmental swabs were collected from surfaces after cleaning and sanitizing. Metataxonomic survey highlighted a negligible impact of fecal contamination and a major role of broiler's skin in determining the composition of the resident abattoir microbiota. The introduction of Arcobacter spp. in the environment was mainly conveyed by this source rather than the intestinal content. Arcobacter butzleri represented one of the most abundant species and was extensively detected in the abattoir by both metataxonomic and enrichment methods, showing higher prevalence than other more thermophilic Campylobacterota. In particular, Arcobacter spp. was recovered viable in the plucking sector with high frequency, despite the adequacy of the sanitizing procedure.IMPORTANCEOur findings have emphasized the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. Although the responses provided here are not conclusive for the identification of the primary source of contamination, this biogeographic assessment underscores the importance of monitoring Arcobacter spp. from the early stages of the production chain with the integrative support of metataxonomic analysis. Through such combined detection approaches, the presence of this pathogen could be soon regarded as hallmark indicator of food safety and quality in poultry slaughtering.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.