Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination.

SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3-1.3 log10 RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R0 of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.

The transmittable through stinging microbiota differs between honeybees and wasps: a potentially greater microbial risk of the wasp sting for humans.

The present research investigated whether accidental contact through stinging with honeybees, wasps, and hornets could represent a microbial hazard for humans. It has been previously suggested that such contact may transmit pathogens causing infections that could even be fatal for some susceptible individuals. Stinging simulation experiments were performed in the lab with live insects collected from the environment in Lemnos Island (north-eastern Greece), while different selective agar media targeting some clinically important bacteria (i.e., Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis/faecium, and Pseudomonas aeruginosa) were used as substrates for microbial recovery and identification. Results revealed none of the target pathogenic bacterial species in the honeybee samples, with bacilli, staphylococci, and micrococci dominating their surveyed microbiota. However, most of the suspect colonies isolated from wasps and hornets belonged to important hygienic indicators (i.e., enterococci, Proteus mirabilis, and coliforms), implying possible contact of these insects with fecal origin materials. To sum up, the microbiota that may be transmitted to humans through stinging appears to differ between honeybees and wasps/hornets, while the isolation from the latter samples of some other important opportunistic pathogens, such as Enterobacter spp. and Klebsiella spp., also known for multidrug resistance, could be an additional reason of concern.

Fish-Derived Protein Hydrolysates Increase Insulin Sensitivity and Alter Intestinal Microbiome in High-Fat-Induced Obese Mice.

Obesity and type 2 diabetes are characterized by low-grade systemic inflammation and glucose intolerance, which can be partially controlled with nutritional interventions. Protein-containing nutritional supplements possess health-promoting benefits. Herein, we examined the effect of dietary supplementation with protein hydrolysates derived from fish sidestreams on obesity and diabetes, utilizing a mouse model of High-Fat Diet-induced obesity and type 2 diabetes. We examined the effect of protein hydrolysates from salmon and mackerel backbone (HSB and HMB, respectively), salmon and mackerel heads (HSH and HMH, respectively), and fish collagen. The results showed that none of the dietary supplements affected weight gain, but HSH partially suppressed glucose intolerance, while HMB and HMH suppressed leptin increase in the adipose tissue. We further analyzed the gut microbiome, which contributes to the metabolic disease implicated in the development of type 2 diabetes, and found that supplementation with selected protein hydrolysates resulted in distinct changes in gut microbiome composition. The most prominent changes occurred when the diet was supplemented with fish collagen since it increased the abundance of beneficial bacteria and restricted the presence of harmful ones. Overall, the results suggest that protein hydrolysates derived from fish sidestreams can be utilized as dietary supplements with significant health benefits in the context of type 2 diabetes and diet-induced changes in the gut microbiome.

Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding.

Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.

Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity.

Metabolic syndrome-related diseases affect millions of people worldwide. It is well established that changes in nutritional habits and lifestyle can improve or prevent metabolic-related pathologies such as type-2 diabetes and obesity. Previous reports have shown that nutritional supplements have the capacity to limit glucose intolerance and suppress diabetes development. In this study, we investigated the effect of dietary supplementation with fish-derived extracts on obesity and type 2 diabetes and their impact on gut microbial composition. We showed that nutritional supplements containing Fish Complex (FC), Fish Complex combined with Cod Powder (FC + CP), or Cod Powder combined with Collagen (CP + C) improved glucose intolerance, independent of abdominal fat accumulation, in a mouse model of diet-induced obesity and type 2 diabetes. In addition, collagen-containing supplements distinctly modulate the gut microbiome in high-fat induced obesity in mice. Our results suggest that fish-derived supplements suppress diet-induced type 2 diabetes, which may be partly mediated through changes in the gut microbiome. Thus, fish-derived supplements and particularly the ones containing fish collagen have potential beneficial properties as dietary supplements in managing type 2 diabetes and metabolic syndrome via modulation of the gut microbiome.

Isoprenoid biosynthesis in the diatom Haslea ostrearia.

Diatoms are eukaryotic, unicellular algae that are responsible for c. 20% of the Earth's primary production. Their dominance and success in contemporary oceans have prompted investigations on their distinctive metabolism and physiology. One metabolic pathway that remains largely unexplored in diatoms is isoprenoid biosynthesis, which is responsible for the production of numerous molecules with unique features. We selected the diatom species Haslea ostrearia because of its characteristic isoprenoid content and carried out a comprehensive transcriptomic analysis and functional characterization of the genes identified. We functionally characterized one farnesyl diphosphate synthase, two geranylgeranyl diphosphate synthases, one short-chain polyprenyl synthase, one bifunctional isopentenyl diphosphate isomerase - squalene synthase, and one phytoene synthase. We inferred the phylogenetic origin of these genes and used a combination of functional analysis and subcellular localization predictions to propose their physiological roles. Our results provide insight into isoprenoid biosynthesis in H. ostrearia and propose a model of the central steps of the pathway. This model will facilitate the study of metabolic pathways of important isoprenoids in diatoms, including carotenoids, sterols and highly branched isoprenoids.

Training a Child with Blindness on the Basic Use of Computer with the Aim of Internet Socialization; an Intervention Program.

In the present intervention program an eleven-year-old student with visual impairments was introduced in the basic use of a computer for the first time. The key tools for achieving this goal were the screen reading software "NVDA" as well as the development of a well-structured educational program. The purpose of the intervention was to enhance the student's technological skills, to make him familiar with the use of assistive technology and to enable him to exploit these new skills for his internet socialization. The evaluation of the intervention program's results was completed on three stages: a) after testing the student's knowledge and skills in the basic use of a computer (pre- and post-assessment ), b) after measuring his social network, his self-esteem and the perceived social support, and c) after analyzing the content of the student's written speech based on a series of criteria. (pre- and post-assessment). The results showed that the basic use of a computer was acquired and internet socialization increased his level of self-esteem, his social network and simultaneously created a sense of belonging. Finally, there was an improvement in his writing.

Microbial and Biochemical Profile of Different Types of Greek Table Olives.

Analysis of table olives microbiome using next-generation sequencing has enriched the available information about the microbial community composition of this popular fermented food. In this study, 16S and 18S rRNA sequencing was performed on table olives of five Greek popular cultivars, Halkidikis, Thassou, Kalamon, Amfissis, and Konservolia, fermented either by Greek style (in brine or salt-drying) or by Spanish style, in order to evaluate their microbial communities. Moreover, analytical methods were used to evaluate their biochemical properties. The prevailing bacterial species of all olives belonged to Lactobacillaceae, Leuconostocaceae, and Erwiniaceae families, while the most abundant yeasts were of the Pichiaceae family. Principal coordinates analysis showed a clustering of samples cured by salt-drying and of samples stored in brine, regardless of their cultivar. The biochemical evaluation of total phenol content, antioxidant activity, hydroxytyrosol, oleuropein, oleocanthal, and oleacein showed that salt-dried olives had low amounts of hydroxytyrosol, while Spanish-style green olives had the highest amounts of oleocanthal. All the other values exhibited various patterns, implying that more than one factor affects the biochemical identity of the final product. The protocols applied in this study can provide useful insights for the final product, both for the producers and the consumers.

Genomic and 16S metabarcoding data of Holothuria tubulosa Gmelin, 1791.

Holothuria tubulosa Gmelin, 1791 is an edible sea cucumber species widespread in the Mediterranean Sea with ecological and increasing economic importance. Genome data of holothurian species is limited and the availability of genomic data resources is crucial in understanding their biology and adaptability mechanisms. This dataset presents the raw genome sequence data of H. tubulosa sequenced on an Illumina NextSeq 2000 platform. Genome size estimation was performed based on k-mer frequency approach. Additionally, the bacterial microbiome in the stomach and intestine of H. tubulosa collected from the Strymonian Gulf (North Aegean Sea, Greece) through 16S rRNA amplicon metabarcoding sequencing is reported. Sequencing was performed on an Illumina MiSeq platform. Analysis was conducted using the QIIME2 software package, the DADA2 algorithm and a trained classifier for taxonomy assignment. The datasets presented in this work serve as valuable resources for a comprehensive investigation of H. tubulosa at the genome level and for comparative genomics and echinoderms gut microbial studies.

A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds.

Genetic selection for higher productivity increased dairy sheep susceptibility to diseases and environmental stressors, challenging their health and welfare status and production efficiency. Improving resilience to such stressors can enhance their ability to face these challenges without compromising productivity. Our objective was to estimate genomic heritability and perform genome-wide association studies (GWAS) to detect SNPs and candidate genes associated with three proxy traits for resilience (milk somatic cell count-SCC, lactation persistency-LP, body condition score-BCS) of Chios and Frizarta dairy ewes. We used genome-wide genotypes of 317 Chios and 346 Frizarta ewes. Individual records of milk yield and BCS, and milk samples were collected monthly for two consecutive milking periods; samples were analyzed to determine SCC. The LP was calculated as the regression coefficient of daily milk yield on days from lambing. Within breed, variance components analyses and GWAS were performed using genomic relatedness matrices in single-trait animal linear mixed models. Genomic-based heritability estimates were relatively high (BCS: h2 = 0.54 and 0.55, SCC: h2 = 0.25 and 0.38, LP: h2 = 0.43 and 0.45, for Chios and Frizarta ewes, respectively), compared to previous pedigree-based studies. The GWAS revealed 7 novel SNPs associated with the studied traits; one genome-wide and two suggestive significant SNPs for SCC (Frizarta: rs403061409, rs424064526 and rs428540973, on chromosomes 9, 1 and 12, respectively), one suggestive significant SNP for BCS (Chios: rs424834097 on chromosome 4) and three suggestive significant SNPs for LP (Frizarta: rs193632931 and rs412648955 on chromosomes 1 and 6, Chios: rs428128299 on chromosome 3). Nineteen candidate genes were detected: two for BCS (Chios: POT1, TMEM229A), thirteen for SCC (Frizarta: NTAQ1, ZHX1, ZHX2, LOC101109545, HAS2, DERL1, FAM83A, ATAD2, RBP7, FSTL1, CD80, HCLS1, GSK3B) and four for LP (Frizarta: GRID2, FAIM, CEP70-Chios: GRIP1). Present results show that resilience in the studied dairy sheep breeds is heritable and advance existing knowledge on the genomic background of SCC, LP, and BCS. Future research will quantify effects of different alleles of significant SNPs on the studied traits and search for possible correlations among traits to facilitate their effective incorporation in breeding programs aiming to improve resilience.

Effects of Dietary Supplementation of Spirulina platensis on the Immune System, Intestinal Bacterial Microbiome and Skin Traits of Mink.

The impact of dietary inclusion of Spirulina platensis on the immune system, intestinal microbiome and skin of mink was investigated. Forty-eight animals were equally separated into four groups. Groups B and D were control animals, while groups A and C had their feed supplemented daily with 100 mg/kg of body weight Spirulina. Mink in groups A and B were descended from dams supplemented with spirulina during their reproductive period, while those in groups C and D were descended from dams fed the control diets. Fur growth rate and quality were graded semi-quantitatively. Fecal microbiome analysis, skin thickness histomorphometry, immunohistochemical labeling and counts of immune cells in the colon, mesenteric lymph nodes and spleen and quantitative gene expression analysis of cytokines in the colon were performed. Skin thickness, fur growth rate and skin quality were similar among groups (p > 0.05). However, differences were observed among groups concerning the relative and differential abundance of bacterial species. Tgf-ß expression was lower in group A, whereas IL-ß1 was lower in group C compared to group B (p < 0.05). Group D had significantly lower numbers of inflammatory cells in the colon and mesenteric lymph nodes. The results revealed that Spirulina decreased indices of subclinical inflammation in mink gut, while differences in the bacterial communities among groups were observed.

Isolation of a CENTRORADIALIS/TERMINAL FLOWER1 homolog in saffron (Crocus sativus L.): characterization and expression analysis.

Genes in the phosphatidyl-ethanolamine-binding protein (PEBP) family are instrumental in regulating the fate of meristems and flowering time. To investigate the role of these genes in the monocotyledonous plant Crocus (Crocus sativus L), an industrially important crop cultivated for its nutritional and medicinal properties, we have cloned and characterized a CENTRORADIALIS/TERMINAL FLOWER1 (CEN/TFL1) like gene, named CsatCEN/TFL1-like, the first reported CEN/TFL1 gene characterized from such a perennial geophyte. Sequence analysis revealed that CsatCEN/TFL1 shows high similarity to its homologous PEBP family genes CEN/TFL1, FT and MFT from a variety of plant species and maintains the same exon/intron organization. Phylogenetic analysis of the CsatCEN/TFL1 amino acid sequence confirmed that the isolated sequences belong to the CEN/TFL1 clade of the PEBP family. CsatCEN/TFL1 transcripts could be detected in corms, flower and flower organs but not in leaves. An alternative spliced transcript was also detected in the flower. Comparison of expression levels of CsatCEN/TFL1 and its alternative spliced transcript in wild type flower and a double flower mutant showed no significant differences. Overexpression of CsatCEN/TFL1 transcript in Arabidopsis tfl1 plants reversed the phenotype of early flowering and terminal flowering of the tfl1 plants to a normal one. Computational analysis of the obtained promoter sequences revealed, next to common binding motifs in CEN/TFL1-like genes as well as other flowering gene promoters, the presence of two CArG binding sites indicative of control of CEN/TFL1 by MADS-box transcription factors involved in crocus flowering and flower organ formation.

Genomic data of two Greek Vitis varieties.

The genetic material of Vitis varieties is crucial for the wine sector. In addition, genomic technologies applied in vitis germplasm characterization are important for the conservation of indigenous genetic reservoirs. Until recently the most common method to genetically identify vitis varieties was the use of Simple Sequence Repeats (SSR) along with SNP chips. Yet, with the progress in Next Generation Sequencing (NGS) technologies and the reduced sequencing cost per base, a twist in plant species genetic identification methods has occurred. Among them, the low coverage Whole-Genome Sequencing (lcWGS) method with downstream bioinformatic analysis for variant discovery and phylogenetic characterization is gaining scientific attention. In this dataset, shotgun sequencing data of two different Greek Vitis varieties, 'Razaki' and 'Vlachiko' are presented. Vitis cultivars were collected from the Aristotle University of Thessaloniki's (AUTH) ampelographic collection and have been previously phenotypically and genetically characterized. WGS libraries were sequenced on an IlluminaⓇ NovaSeq 6000 platform with the IlluminaⓇ NovaSeq 6000 S2 Reagent Kit (300 cycles). Raw sequence data used for analysis are available in NCBI under the Sequence Read Archive (SRA), with BioProject ID PRJNA805368. Reads were aligned to the reference genome of Vitis vinifera available from the EnsemblPlants database and formal analysis was conducted with the Genome Analysis Toolkit 4 (GATK4) pipeline. Data can be used to enrich our knowledge related to the genetic background of vitis cultivars and can also serve as a threshold in the scientific community towards the construction of a genomic database of vitis cultivars.

Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds.

In dairy sheep industry, milk production dictates the value of a ewe. Milk production is directly related to the morphology and physiology of the mammary gland; both being designated targets of breeding strategies. Although within a flock breeding parameters are mutual, large differences in milk production among individual ewes are usually observed. In this work, we tested two of the most productive dairy sheep breeds reared intensively in Greece, one local the Chios breed and one foreign the Lacaune breed. We used transcriptome sequencing to reveal molecular mechanisms that render the mammary gland highly productive or not. While highly expressed genes (caseins and major whey protein genes) were common among breeds, differences were observed in differentially expressed genes. ENSOARG00000008077, as a member of ribosomal protein 14 family, together with LPCAT2, CCR3, GPSM2, ZNF131, and ASIP were among the genes significantly differentiating mammary gland's productivity in high yielding ewes. Gene ontology terms were mainly linked to the inherent transcriptional activity of the mammary gland (GO:0005524, GO:0030552, GO:0016740, GO:0004842), lipid transfer activity (GO:0005319) and innate immunity (GO:0002376, GO:0075528, GO:0002520). In addition, clusters of genes affecting zinc and iron trafficking into mitochondria were highlighted for high yielding ewes (GO:0071294, GO:0010043). Our analyses provide insights into the molecular pathways involved in lactation between ewes of different performances. Results revealed management issues that should be addressed by breeders in order to move toward increased milk yields through selection of the desired phenotypes. Our results will also contribute toward the selection of the most resilient and productive ewes, thus, will strengthen the existing breeding systems against a spectrum of environmental threats.

Amplicon metabarcoding data of prokaryotes and eukaryotes present in 'Kalamata' table olives packaged under modified atmosphere.

Evaluation of food microbiome is of major importance since it accounts for the product's organoleptic characteristics and their nutritional value. In this dataset, microbes present in olive samples ('Kalamata' variety) stored under modified atmosphere and throughout different time-points of the shelf life of the product are presented, originated after 16S and 18S rRNA sequencing. The different time-points analyzed were: T0 (immediately after packaging), T6 (six months of storage), T12 (12 months of storage) and T18 (six months after the end of shelf life). Sequencing was performed on a MiSeq platform with the MiSeq Reagent Kit v3 (600 cycles). The raw sequence data used for analysis are available in NCBI under the Sequence Read Archive (SRA), with BioProject ID PRJNA688686. Raw reads were analyzed using the QIIME2 pipeline, clustered into Operational Taxonomic Units (OTU) and aligned against SILVA 132 reference database. OTUs are presented in different taxonomic levels for each time-point. These data present valuable information on the microbial communities of table olives, a dynamic niche that affect the final product quality. The data presented are related to the research article "Insights into the evolution of Greek style table olives microbiome stored under modified atmosphere: biochemical implications on the product quality" [1].

Characterization of Artisanal Spontaneous Sourdough Wheat Bread from Central Greece: Evaluation of Physico-Chemical, Microbiological, and Sensory Properties in Relation to Conventional Yeast Leavened Wheat Bread.

In the present study, both yeast leavened bread (YLB) and artisanal sourdough wheat bread (SDB) were prepared. The physico-chemical, microbiological, and sensory properties of breads were monitored as a function of storage time (T = 25 °C). As expected, the titratable acidity (TA) values of SDB were higher than those of YLB. The aroma profile of SDB was similar to that of YLB, including classes of compounds such as alcohols, aldehydes, ketones, esters, organic acids, terpenes, and sulfur compounds; however, the concentrations between the two were different. Aroma deterioration of bread during storage was partly related to the loss of several volatiles. Texture and sensory analysis showed that SDB was harder, less elastic, but richer in aroma and light sour taste than YLB. Mold growth was apparent when the population of yeasts/molds reached approximately 4 log cfu/g. This yeast/mold count was reached on days 4-5 for YLB and day 18 + for SDB. A 16S amplicon meta-barcoding analysis showed that the bacterial profile of SDB was dominated by a single genus, (Lactobacillus). Analysis of the eukaryotic load showed that at the genus level, Saccharomyces and Alternaria were the most abundant genera, independently of the gene sequenced (18S or ITS). Based primarily on mold growth and texture data, which proved to be the most sensitive quality parameters, the shelf life was ca. 4-5 days for YLB and 10 days for SDB.

Investigating Transcriptomic Induction of Resistance and/or Virulence in Listeria monocytogenes Cells Surviving Sublethal Antimicrobial Exposure.

The potential transcriptomic induction of resistance and/or virulence in two L. monocytogenes strains belonging to the most frequent listeriosis-associated serovars (i.e., 1/2a and 4b), following their sublethal antimicrobial exposure, was studied through qPCR determination of the relative expression of 10 selected related genes (i.e., groEL, hly, iap, inlA, inlB, lisK, mdrD, mdrL, prfA, and sigB). To induce sublethal stress, three common antimicrobials (i.e., benzalkonium chloride, thymol, and ampicillin) were individually applied for 2 h at 37 °C against stationary phase cells of each strain, each at a sublethal concentration. In general, the expression of most of the studied genes remained either stable or was significantly downregulated following the antimicrobial exposure, with some strain-specific differences to be yet recorded. Thymol provoked downregulation of most of the studied genes, significantly limiting the expression of 6/10 and 4/10 genes in the strains of ser. 1/2a and ser. 4b, respectively, including those coding for the master regulators of stress response and virulence (SigB and PrfA, respectively), in both strains. At the same time, the two genes coding for the invasion internalin proteins (InlA and InlB), with crucial role in the onset of L. monocytogenes pathogenesis, were both importantly upregulated in ser. 4b strain. The results obtained increase our knowledge of the stress physiology of L. monocytogenes under certain sublethal antimicrobial conditions that could be encountered within the food chain and in clinical settings, and may assist in better and more effective mitigation strategies.

Effects of Magnesium Oxide and Magnesium Hydroxide Microparticle Foliar Treatment on Tomato PR Gene Expression and Leaf Microbiome.

Recently, metal oxides and magnesium hydroxide nanoparticles (NPs) with high surface-to-volume ratios were shown to possess antibacterial properties with applications in biomedicine and agriculture. To assess recent observations from field trials on tomatoes showing resistance to pathogen attacks, porous micron-scale particles composed of nano-grains of MgO were hydrated and sprayed on the leaves of healthy tomato (Solanum lycopersicum) plants in a 20-day program. The results showed that the spray induced (a) a modest and selective stress gene response that was consistent with the absence of phytotoxicity and the production of salicylic acid as a signalling response to pathogens; (b) a shift of the phylloplane microbiota from near 100% dominance by Gram (-) bacteria, leaving extremophiles and cyanobacteria to cover the void; and (c) a response of the fungal leaf phylloplane that showed that the leaf epiphytome was unchanged but the fungal load was reduced by about 70%. The direct microbiome changes together with the low level priming of the plant's immune system may explain the previously observed resistance to pathogen assaults in field tomato plants sprayed with the same hydrated porous micron-scale particles.

Microbiota and volatilome profile of fresh and chill-stored deepwater rose shrimp (Parapenaeus longirostris).

Bacterial communities and Volatile Organic Compounds (VOCs) profile of deepwater rose shrimp (Parapenaeus longirostris) stored at 0 °C (ice) and 4 °C were investigated using 16S amplicon based sequencing and Solid phase micro-extraction (SPME) - Gas chromatography/mass spectrometry (GC/MS), respectively. The shelf-life of shrimps determined by sensory assessment was 5 and 2 days at 0 °C and 4 °C, respectively. Based on 16S analysis (culture-independed), the initial microbiota of shrimps mainly consists of Photobacterium, Candidatus Hepatoplasma, Psychrobacter, Acinetobacter and Delftia. Psychrobacter and Carnobacterium dominated during storage at both temperatures. Psychrobacter was the most dominant taxon at the end of shelf-life of chill-stored shrimps. A minor microbial population composed by Brevundimonas, Stenotrophomonas, Staphylococcus, Legionella, Acinetobacter, Bacillus, Escherichia-Shigella, Enterococcus, Enterobacter, Klebsiella was also detected. Those taxa may be originated from the environment due to an inadequate hygienic practice during fishing, handling and icing. VOCs such as ethanol, 3-methyl-1-butanol, 2-ethyl-1-hexanol, 3-hydroxy-2-butanone, indole etc., were found to be associated with shrimps at 4 °C, while acetone and dimethyl sulfide with shrimps in ice. Some VOCs, from microbial or chemical origin, increased in shrimps either at 0 °C (i.e. 1-octen-3-ol, trans-2-octenal) or at 4 °C (i.e. 3-methyl-1-butanol, indole), while 2-methylbutanal and 3-methylbutanal increased in both temperatures. A positive correlation between Psychrobacter with 2-ethyl-1-hexanol and Carnobacterium with 3-methyl-1-butanol was also observed. Concluding, we suggest the reinforcement of Good Hygiene Practices on fishing boats during fishing/handling, the rapid onboard icing and keeping shrimps iced avoiding even small increase of storage temperature that affects quality parameters (e.g. microbial population level, synthesis of microbiota, VOCs profile) in order to provide a product of the highest quality and safety in the market.