Untangling the cephalopod market: Authentication of seafood products in Greece with DNA-barcoding

Cephalopod products are very popular in Greece and are considered a delicacy. However, heavy processing and marketing practices interfere with visual inspection and impede morphological identification, allowing species substitution. Mislabeling of seafood products remains a worldwide issue despite existing labeling regulations at local and European level. For the detection of fraudulent products, a variety of identification methods have been developed, however DNA barcoding remains the most favored. This study aims to investigate the cephalopod species sold in the country's seafood market and assess their mislabeling rates. Two mitochondrial genes, the cytochrome c oxidase subunit I (COI) and the 16S ribosomal RNA (16S), were selected for the analyses. A total of 156 samples were collected from fishmongers, markets, and restaurants across four cities. Identification was successful in 93.58% of the samples and 59 discrepancies (40.41%) between the label and the identified species were recorded. However, in some cases, substitution might have been unintentional, caused by negligence, lack of detailed information on the label, and the overall low awareness of the legislation by retailers. High mislabeling rates were estimated, especially when compared against the average global substitution rate in seafood products but align with those reported by studies on cephalopod products. This study is the first to investigate mislabeling rates in cephalopod commodities in Greece. With the aim of a transparent seafood trade, our results highlight the need for monitoring of all seafood products available in the country's market

Genetic diversity and adaptability of native sheep breeds from different climatic zones

To better understand the genetic architecture and adaptability of native sheep, 22 breeds were genotyped using ovine50K SNP chips. Eleven additional populations from open-source repositories were included. Cross population Extended Haplotype Homozygosity (XP-EHH) and Relative Scaled Haplotype Homozygosity (Rsb) haplotype-based approaches were used to identify genetic variations influencing the adaptation of local sheep breeds to different climatic zones. The results indicate that all breeds exhibited high but declining genetic diversity levels, with a larger proportion of genetic variation explained by development history and refined by geographical origin, as shown by principal component analysis and Neighbor Net graphs. Admixture analysis revealed high admixture levels in European and North African breeds. Using XP-EHH and Rsb methods, 371 genes were putatively under selection, with only nine common among all population pairs, highlighting unique adaptability. Most identified genes, including Interleukin (IL) and cluster differentiation (CD) gene families underlie immune responses, emphasizing their role in resilience to climate change effects. These findings support that indigenous sheep breeds have retained significant genetic diversity, but improper genetic management may threaten it. Additionally, the research emphasizes that indigenous sheep breeds’ unique adaptability to specific climatic zones makes them valuable genetic assets for developing climate-resilient breeds

Quantitative Trait Loci Involved in Sex Determination and Body Growth in the Gilthead Sea Bream (Sparus aurata L.) through Targeted Genome Scan

Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443–HQ021749.

Διερεύνηση σχημάτων επιλογής που αξιοποιούν μεθόδους ποσοτικής και μοριακής γενετικής για την βελτίωση της καλλιεργούμενης τσιπούρας (Sparus aurata L.)

In the present PhD thesis, the available seabream molecular genetic resources were utilized to conduct a partial genome scan for locating possible QTL linked to sex, body weight and eighteen other morphometric characters. For that reason, microsatellite markers were chosen from the existing genetic linkage maps of S. aurata, in order to cover nine linkage groups (LG1, 2, 3, 6, 9, 10, 21, 23 and 25). In total, 74 informative microsatellites were genotyped on 58 brooders and 409 offspring (360 males and 49 females), comprising ten paternal half-sib families. Given the pedigree structure, the QTL detection method was based on half-sib interval mapping analysis through a linear regression approach. The QTL scan was also linked to results retrieved through comparative analysis to other fish species, where candidate regions for sex determination and growth were proposed.Chromosome-wide and genome-wide significant evidence for QTL segregation within the ten chosen paternal half-sib families was found on seven (1, 6, 9, 10, 21, 23 and 25) out of nine examined linkage groups. In total, four QTL affecting body weight and six QTL affecting morphology (using body weight as a covariate) were detected under the assumption of the one-QTL model, while six sex-related QTL were identified under the two-QTL model of analysis (three pairs in three different LGs). Comparison of two-QTL vs. one-QTL model showed that the one-QTL model was of better fit for body weight and morphology QTL while the two-QTL model was of better fit for sex-linked QTL. The proportion of phenotypic variation explained by all the identified QTL herein was medium to high, ranging from 9.3 to 28.7%.Body weight was significantly associated at a genome-wide scale with two QTL positioned on linkage groups 1 and 21 (qBW1 and qBW21, respectively), exhibiting large fractions of phenotypic variance explained (14.8% and 17.2%, correspondingly). Moreover, when fitting body weight as a covariate in the analysis, six QTL affecting morphometric characters were detected. The results herein combined with those from other studies reveal highly significant QTL affecting both morphology and bodyweight in gilthead seabream; this highlights the great potential for the implementation of selective breeding programs (through the combination of Marker Assisted Selection-MAS and classical selection) that focus on improvement of S. aurata overall growth, including size and shape. Finally, the mechanism of S. aurata sex change is thought to be controlled up to date by time (reversal occurs after the second year of life) as well as social and group dynamics. The present thesis, however, provides strong evidence for the existence of genetic control in sex reversal for this teleost fish.Στην παρούσα διδακτορική διατριβή χρησιμοποιήθηκαν κάποια από τα διαθέσιμα μοριακά και γονιδιωματικά «εργαλεία» που υπάρχουν στην τσιπούρα, προκειμένου να διεξαχθεί μία μελέτη ανίχνευσης των QTL που επηρεάζουν το σωματικό βάρος, το φύλο και 18 ακόμη μορφομετρικούς χαρακτήρες, καλύπτοντας ένα μεγάλο μέρος του γονιδιώματος του είδους. Για το λόγο αυτό χρησιμοποιήθηκαν μικροδορυφορικοί δείκτες από τους υπάρχοντες γενετικούς χάρτες σύνδεσης της τσιπούρας ώστε να καλύψουν εννέα ομάδες σύνδεσης (1, 2, 3, 6, 9, 10, 21, 23 και 25). Συνολικά έγινε γονοτύπηση με 74 μικροδορυφόρους σε 58 γονείς και 409 απογόνους (360 αρσενικά και 49 θηλυκά άτομα), οι οποίοι σχημάτιζαν δέκα ετεροθαλείς οικογένειες έχοντας για κοινό γονέα αρσενικό άτομο. Δεδομένης της δομής των οικογενειών, η μέθοδος ανίχνευσης QTL βασίστηκε στην ανάλυση διαστήματος μέσω της γραμμικής παλινδρόμησης. Η μελέτη για τον εντοπισμό QTL βασίστηκε επίσης σε αποτελέσματα συγκριτικής χαρτογράφησης του γονιδιώματος της τσιπούρας με γονιδιώματα άλλων ειδών, για τα οποία έχουν βρεθεί γονιδιακοί τόποι που επηρεάζουν το φύλο και την ανάπτυξη.Στατιστικά σημαντική απόδειξη για την ύπαρξη QTL, στις δέκα υπό μελέτη ετεροθαλείς οικογένειες, βρέθηκε σε εφτά (1, 6, 9, 10, 21, 23 και 25) από τις εννέα ομάδες σύνδεσης που αναλύθηκαν. Συνολικά βρέθηκαν τέσσερα QTL που επηρεάζουν το βάρος, έξι QTL που σχετίζονται με μορφομετρικούς χαρακτήρες (χρησιμοποιώντας το βάρος ως συμμεταβλητή) και τρία ζεύγη QTL που επηρεάζουν το φύλο (σε τρεις διαφορετικές ομάδες σύνδεσης). Το ποσοστό της φαινοτυπικής παραλλακτικότητας που εξηγείται από τα ανιχνευθέντα QTL ήταν μέτριο ως υψηλό, κυμαινόμενο από 9.3 έως 28.7%.Το σωματικό βάρος βρέθηκε να είναι στατιστικώς σημαντικά συνδεδεμένο σε επίπεδο γονιδιώματος με δύο QTL ευρισκόμενα στις ομάδες σύνδεσης 1 και 21 (qBW1 και qBW21, αντίστοιχα). Επιπλέον, όταν χρησιμοποιήθηκε το βάρος ως συμμεταβλητή στην ανάλυση, εντοπίστηκαν έξι QTL που επηρεάζουν μορφομετρικές ιδιότητες. Τα αποτελέσματα της παρούσας διατριβής σε συνδυασμό με αυτά διαφόρων άλλων παρεμφερών επιστημονικών μελετών αποκαλύπτουν την ύπαρξη QTL με στατιστικά σημαντικές τιμές που επηρεάζουν το βάρος και τη μορφολογία στη τσιπούρα. To γεγονός αυτό καταδεικνύει τη μεγάλη δυναμική που υπάρχει για την εφαρμογή προγραμμάτων επιλογής (μέσω του συνδυασμού Marker Assisted Selection–MAS και κλασσικής επιλογής) που θα στοχεύουν στη γενετική βελτίωση του μεγέθους και του σχήματος στην τσιπούρα. Τέλος, ο μηχανισμός αλλαγής του φύλου στην τσιπούρα πιστεύεται μέχρι σήμερα ότι ελέγχεται από παράγοντες κοινωνικής δομής καθώς και παράγοντες δυναμικής πληθυσμών. Παρόλα αυτά, τα αποτελέσματα της παρούσας διατριβής αναδεικνύουν την ύπαρξη γενετικού ελέγχου στην αναστροφή φύλου του συγκεκριμένου είδους

Influence of Oregano Essential Oil on the Rumen Microbiome of Organically Reared Alpine Goats: Implications for Methanobacteria Abundance

The present study aimed to evaluate the effects of dietary supplementation with organic oregano (Origanum vulgare) essential oil (OEO) on the rumen microbial population, with a focus on methanogenic archaea, in lactating dairy goats. A total of nine age-matched goats (mean body weight 49 ± 1.8 kg) were assigned to three experimental groups (n = 3 per group) in a completely randomized design. All animals were fed a basal diet consisting of a corn-based concentrate and a forage mix composed of alfalfa hay, wheat straw and corn silage. Group 1 was the control group while Groups 2 and 3 received an OEO supplement at dosages of 1 mL/day and 2 mL/day per animal, respectively, incorporated into the concentrate feed. Rumen fluid samples were collected on days 15, 30 and 45 of the feeding trial and their microbial profile was assessed using NGS analysis. The results demonstrated a reduction in the relative abundance of methanobacteria in both OEO-supplemented groups compared to the control group. Statistical analysis revealed significant differences between feeding groups and days of sampling. These findings suggest that OEO has the potential to modulate the rumen microbiome by reducing methane-producing archaeal populations. In conclusion, dietary supplementation with OEO may serve as a natural strategy to mitigate enteric methane emissions in Alpine dairy goats

Microbiome Profile of the Mediterranean Mussel (Mytilus galloprovincialis) from Northern Aegean Sea (Greece) Culture Areas, Based on a 16S rRNA Next Generation Sequencing Approach

Mediterranean mussels (Mytilus galloprovincialis), due to their nutritional mechanisms which involve filtering huge amounts of water, are affected by seawater pollution and can host microbial diversity of environmental origin, as well as pathogenic bacteria that must be constantly monitored. Herein, we applied a Next Generation Sequencing (NGS) metabarcoding approach in order to study the M. galloprovincialis microbiota. Collection of samples was conducted during winter and summer months from various mussel farm zones located in specific farm regions in the Thermaikos gulf, the northern Aegean Sea, Greece. A microbiological test was performed for the enumeration of Escherichia coli and the presence of Salmonella sp. DNA extraction and amplification of the whole bacterial 16S rRNA gene, followed by NGS amplicon sequencing and taxonomic classification, were carried out. Statistically significant differences (p &lt; 0.05) in the abundance of the most dominant bacterial phyla, families and genera between winter and summer time periods, regions, as well as zones within each region of sampling, were evaluated with z-score computation. According to the obtained results, the most prevalent taxa at the genus level were Mycoplasma (12.2%), Anaplasma (5.8%), Ruegeria (5.2%) and Mariniblastus (2.1%). Significant differences in the abundance of the most dominant genera were found at all levels of comparison (seasons, regions and zones within each region), highlighting the dynamic character of microorganisms, which might be affected by microenvironmental, temporal and spatial changes. The present research contributes to the characterization of M. galloprovincialis microbiome in areas that have not been studied previously, setting the baseline for future, more thorough investigations of the specific bivalve species and its bacterial profile in the above geographic regions.</jats:p

Utility of dairy microbiome as a tool for authentication and traceability

UTILITY OF DAIRY MICROBIOME AS A TOOL FOR AUTHENTICATION AND TRACEABILITY Open life sciences (Rights reserved) (-) Utility of dairy microbiome as a tool for authentication and traceability / Alvanou, Maria V. (CC BY) (-

Microbiome Profile of the Mediterranean Mussel (Mytilus galloprovincialis) from Northern Aegean Sea (Greece) Culture Areas, Based on a 16S rRNA Next Generation Sequencing Approach

Mediterranean mussels (Mytilus galloprovincialis), due to their nutritional mechanisms which involve filtering huge amounts of water, are affected by seawater pollution and can host microbial diversity of environmental origin, as well as pathogenic bacteria that must be constantly monitored. Herein, we applied a Next Generation Sequencing (NGS) metabarcoding approach in order to study the M. galloprovincialis microbiota. Collection of samples was conducted during winter and summer months from various mussel farm zones located in specific farm regions in the Thermaikos gulf, the northern Aegean Sea, Greece. A microbiological test was performed for the enumeration of Escherichia coli and the presence of Salmonella sp. DNA extraction and amplification of the whole bacterial 16S rRNA gene, followed by NGS amplicon sequencing and taxonomic classification, were carried out. Statistically significant differences (p &lt; 0.05) in the abundance of the most dominant bacterial phyla, families and genera between winter and summer time periods, regions, as well as zones within each region of sampling, were evaluated with z-score computation. According to the obtained results, the most prevalent taxa at the genus level were Mycoplasma (12.2%), Anaplasma (5.8%), Ruegeria (5.2%) and Mariniblastus (2.1%). Significant differences in the abundance of the most dominant genera were found at all levels of comparison (seasons, regions and zones within each region), highlighting the dynamic character of microorganisms, which might be affected by microenvironmental, temporal and spatial changes. The present research contributes to the characterization of M. galloprovincialis microbiome in areas that have not been studied previously, setting the baseline for future, more thorough investigations of the specific bivalve species and its bacterial profile in the above geographic regions

Test-Retest Reliability of PODOSmart® Gait Analysis Insoles

It is recognized that gait analysis is a powerful tool used to capture human locomotion and quantify the related parameters. PODOSmart® insoles have been designed to provide accurate measurements for gait analysis. PODOSmart® insoles are lightweight, slim and cost-effective. A recent publication presented the characteristics and data concerning the validity of PODOSmart® insoles in gait analysis. In literature, there is still no evidence about the repeatability of PODOSmart® gait analysis system. Such evidence is essential in order to use this device in both research and clinical settings. The aim of the present study was to assess the repeatability of PODOSmart® system. In this context, it was hypothesized that the parameters of gait analysis captured by PODOSmart® would be repeatable. In a sample consisting of 22 healthy male adults, participants performed two walking trials on a six-meter walkway. The ICC values for 28 gait variables provided by PODOSmart® indicated good to excellent test-retest reliability, ranging from 0.802 to 0.997. The present findings confirm that PODOSmart® gait analysis insoles present excellent repeatability in gait analysis parameters. These results offer additional evidence regarding the reliability of this gait analysis tool.</jats:p