Persistent Dysbiosis, Parasite Rise and Growth Impairment in Aquacultured European Seabass after Oxytetracycline Treatment.

The use of antibiotics in open-water aquaculture is often unavoidable when faced with pathogens with high mortality rates. In addition, seasonal pathogen surges have become more common and more intense over the years. Apart from the apparent cost of antibiotic treatment, it has been observed that, in aquaculture practice, the surviving fish often display measurable growth impairment. To understand the role of gut microbiota on the observed growth impairment, in this study, we follow the incidence of Photobacterium damselae subsp. piscicida in a seabass commercial open-water aquaculture setting in Galaxidi (Greece). Fish around 10 months of age were fed with feed containing oxytetracycline (120 mg/kg/day) for twelve days, followed by a twelve-day withdrawal period, and another eighteen days of treatment. The fish were sampled 19 days before the start of the first treatment and one month after the end of the second treatment cycle. Sequencing of the 16S rRNA gene was used to measure changes in the gut microbiome. Overall, the gut microbiota community, even a month after treatment, was highly dysbiotic and characterized by very low alpha diversity. High abundances of alkalophilic bacteria in the post-antibiotic-treated fish indicated a rise in pH that was coupled with a significant increase in gut parasites. This study's results indicate that oxytetracycline (OTC) treatment causes persistent dysbiosis even one month after withdrawal and provides a more suitable environment for an increase in parasites. These findings highlight the need for interventions to restore a healthy and protective gut microbiome.

Use of an Innovative Silage of Agro-Industrial Waste By-Products in Pig Nutrition: A Pilot Study of Its Effects on the Pig Gastrointestinal Microbiota.

The aim of this study was to evaluate whether dietary supplementation with an innovative silage (IS) created using 60% olive mill waste, 20% grape pomace, and 20% deproteinised feta cheese waste solids can modulate the composition of the intestinal microbiota in weaned (Exp. 1) and finishing (Exp. 2) pigs. In Exp. 1 (40 day supplementation), forty-five crossbred weaned pigs were randomly assigned to the 0% (Control), 5%, or 10% IS groups (15 replicates/experimental diet). In Exp. 2 (60 day supplementation), eighteen finishing pigs from Exp. 1 were fed the control diet for 8 weeks before being re-assigned to their original experimental groups and fed with the 0% (Control), 5%, or 10% IS diets (six replicates/experimental diet). Performance parameters were recorded. Ileal and caecal digesta and mucosa were collected at the end of each experiment for microbiota analysis using 16S rRNA gene sequencing (five pigs/experimental diet for Exp. 1 and six pigs/experimental diet for Exp. 2). No significant effects on pig growth parameters were observed in both experiments. In Exp. 1, 5% IS supplementation increased the relative abundance of the Prevotellaceae family, Coprococcus genus, and Alloprevotella rava (OTU_48) and reduced the relative abundance of Lactobacillus genus in the caecum compared to the control and/or 10% IS diets (p < 0.05). In Exp. 2, 5% IS supplementation led to compositionally more diverse and different ileal and caecal microbiota compared to the control group (p < 0.05; p = 0.066 for ß-diversity in ileum). Supplementation with the 5% IS increased the relative abundance of Clostridium celatum/disporicum/saudiense (OTU_3) in the ileum and caecum and Bifidobacterium pseudolongum (OTU_17) in the caecum and reduced the relative abundance of Streptococcus gallolyticus/alactolyticus (OTU_2) in the caecum compared to the control diet (p < 0.05). Similar effects on C. celatum/disporicum/saudiense and S. gallolyticus/alactolyticus were observed with the 10% IS diet in the caecum (p < 0.05). IS has the potential to beneficially alter the composition of the gastrointestinal microbiota in pigs.

An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota.

The purpose of this study was to determine for the first time the microbiota in artisanal-type and industrial-type Gidotyri cheeses and investigate the influence of the cheese-making practices on their composition using culture-independent techniques. The microbiota present in artisanal with commercial starters (Artisanal_CS, n = 15), artisanal with in-house starters (Artisanal_IHS, n = 10) and industrial (Ind., n = 9) Gidotyri cheese samples were analyzed using a targeted metagenomic approach (16S rRNA gene). The Ind. Gidotyri cheese microbiota were less complex, dominated by the Streptococcaceae family (91%) that was more abundant compared to the artisanal Gidotyri cheeses (p < 0.05). Artisanal cheeses were more diverse compositionally with specific bacterial species being prevalent to each subtype. Particularly, Loigolactobacillus coryniformis (OTU 175), Secundilactobacillus malefermentans (OTU 48), and Streptococcus parauberis (OTU 50) were more prevalent in Artisanal_IHS cheeses compared to Artisanal_CS (p ≤ 0.001) and Ind. (p < 0.01) Gidotyri cheeses. Carnobacterium maltaromaticum (OTU 23) and Enterobacter hormaechei subsp. hoffmannii (OTU 268) were more prevalent in Artisanal_CS cheeses compared to Artisanal_IHS cheeses (p < 0.05) and Ind. cheeses (p < 0.05). Hafnia alvei (OTU 13) and Acinetobacter colistiniresistens (OTU 111) tended to be more prevalent in Artisanal_CS compared to the other two cheese groups (p < 0.10). In conclusion, higher microbial diversity was observed in the artisanal-type Gidotyri cheeses, with possible bacterial markers specific to each subtype identified with potential application to traceability of the manufacturing processes' authenticity and cheese quality.

Effects of Dietary Omega-3 Enrichment on the Chemical Composition and the Pathogenic Microbiota of Ovine Milk.

The demand for ovine milk and ovine dairy products is constantly increasing due to their exceptional sensorial characteristics and their health benefits for consumers. However, dairy fat content and composition are of particular concern for consumers as well as the medical community, as there are risk factors for coronary disease, diabetes mellitus, cancer, and other serious diseases. For this reason, attempts have been made to control/regulate the fat composition of ovine milk by modifying sheep dietary intake of polyunsaturated fatty acids. In this experimental trial, a group of sheep were fed for 30 days a diet enriched in flaxseeds and lupines, feed ingredients rich in omega-3 fatty acids, aiming to investigate the effects on fat composition and the microbiota of ovine milk. Chemical analysis of the collected milk showed that the omega-3 and omega-6 content was increased. On the opposite, the atherogenic and thrombogenic indexes decreased. Of importance was the semi-protective effect on the udder by the increased omega-3 dietary intake, as depicted by its impact on the biodiversity of the pathogenic microbiota. These findings suggest that ovine milk could be modified under specific conditions to be more appropriate for the consumption by people belonging to high-risk groups for various diseases.

Antimicrobial and Methicillin Resistance Pattern of Potential Mastitis-Inducing Staphylococcus aureus and Coagulase-Negative Staphylococci Isolates from the Mammary Secretion of Dairy Goats.

Staphylococcus spp. is an important mastitis-inducing zoonotic pathogen in goats and is associated with antimicrobial resistance (AMR). The objectives of this study were to determine the prevalence and composition of staphylococci in individual mammary secretion (MS) samples of clinically healthy goats and to evaluate the phenotypic AMR pattern and the presence of methicillin resistance in the Staphylococcus spp. strains. Staphylococcus spp. isolates (n = 101) from the MS samples (n = 220) were identified to species level using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The antimicrobial susceptibility testing included a disk diffusion assay and the determination of the minimum inhibitory concentrations (MIC) of resistant strains (n = 46). Presumptive methicillin-resistant strains (n = 9) were assessed for the presence of mecA, mecC and SCCmec/orfx genes. Staphylococcus spp. isolates were recovered from 45.9% of the MS samples, of which, 72.3% was identified as coagulase-negative staphylococci (CoNS), with the remaining being Staphylococcus aureus. CoNS and S. aureus were most commonly resistant to ampicillin (56.2% and 57.1%, respectively), penicillin (26.0% and 39.3%, respectively), amoxicillin (26 % and 25 %, respectively) and cephalexin (12.3% and 25%, respectively) in the disk diffusion method. CoNS exhibited a broader AMR pattern and a higher percentage of resistant strains than S. aureus in the disk diffusion and MIC methods. Of the nine oxacillin- and cefoxitin-resistant strains, three S. aureus and five CoNS strains carried the mecA gene and, thus, were identified as methicillin-resistant. The mecC gene was not found in any of the studied strains. The presence of AMR and methicillin resistance in caprine S. aureus and CoNS poses a concern for animal and public health.

Impact of an Omega-3-Enriched Sheep Diet on the Microbiota and Chemical Composition of Kefalograviera Cheese.

Kefalograviera is a well-known hard Greek cheese. The aim of this study was to determine how milk produced from ewes fed omega-3-enriched diets could influence the microbiota as well as the chemical composition of Kefalograviera cheese. At the start of the trial, 30 dairy ewes (Lesvos and Chios crossbreed) were selected and fed a conventional diet, based on alfalfa hay, straw and concentrate feed that contained soybean meal for a period of thirty days. Then, for a period of sixty days the same ewes were fed an omega-3-enriched concentrate feed with a lower level of soybean meal that contained 10% flaxseed and 10% lupins. Milk yield was collected individually on Days 30, 60 and 90 and used to produce three different batches of Kefalograviera cheeses, at the same cheese factory, by using a traditional recipe and identical preparation conditions (pasteurization of milk, salt, rennet and culture). Sample analysis was done after six months of Kefalograviera cheese ripening. MALDI-TOF-MS (matrix-assisted laser desorption/ionization time of flight mass spectrometry) identification was performed by contrasting the samples' mass spectra with the corresponding reference database. The correlation between the different Kefalograviera cheeses revealed the predominant species being Lactococcus lactis, Lactobacillus rhamnosus, Lactobacillus plantarum, Lactobacillus brevis, Lactobacillus paracasei, Enterococcus faecium and Enterococcus faecalis, with significant quantitative differences between the experimental groups and the controls. Pediococcus spp. was isolated only from the experimental groups' cheeses and Staphylococcus spp. only from the controls' cheese, suggesting-among other differences-a bacterial microbiota distinction between the groups. Moreover, increased levels of alpha-linolenic acid and total polyunsaturated omega-3 fatty acids were noted in the enriched Kefalograviera cheeses. These promising findings suggest that enriched Kefalograviera cheese could be manufactured via enriching the ewes' diets, with potential benefits for the consumers' health.

The "Crosstalk" between Microbiota and Metabolomic Profile of Kefalograviera Cheese after the Innovative Feeding Strategy of Dairy Sheep by Omega-3 Fatty Acids.

The purpose of this study was to examine the effects of two different feeding systems, a control or a flaxseed and lupin diet (experimental), for a sheep flock, on the microbiota and metabolome of Kefalograviera cheese samples produced by their milk. In particular, the microbiota present in Kefalograviera cheese samples was analyzed using 16S rRNA gene sequencing, while ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was applied to investigate the chemical profile of the cheeses, considering the different feeding systems applied. The metagenomic profile was found to be altered by the experimental feeding system and significantly correlated to specific cheese metabolites, with Streptococcaceae and Lactobacillaceae establishing positive and negative correlations with the discriminant metabolites. Overall, more than 120 features were annotated and identified with high confidence level across the samples while most of them belonged to specific chemical classes. Characteristic analytes detected in different concentrations in the experimental cheese samples including arabinose, dulcitol, hypoxanthine, itaconic acid, L-arginine, L-glutamine and succinic acid. Therefore, taken together, our results provide an extensive foodomics approach for Kefalograviera cheese samples from different feeding regimes, investigating the metabolomic and metagenomic biomarkers that could be used to foresee, improve, and control cheese ripening outcomes, demonstrating the quality of the experimental Kefalograviera cheese.

Identification by MALDI-TOF MS and Antibiotic Resistance of Riemerella anatipestifer, Isolated from a Clinical Case in Commercial Broiler Chickens.

The Gram-negative bacterium Riemerella anatipestifer (RA) is known to cause clinical disease with severe economic impacts primarily in ducks and less frequently in geese and turkeys. RA was isolated and identified in broiler chickens, from a clinical case in a commercial broiler farm located in the southwest mainland of Greece. The morbidity and the mortality in the broiler house were estimated at 10% and 5% respectively. The observed clinical signs appeared at the age of 30 to 42 days with respiratory distress (dyspnea), white fluid feces and stunting. Post-mortem examinations displayed serositis, pericarditis, perihepatitis and airsacculitis. Edematous swelling around the tibio-tarsal joints was observed in some birds. Tissue samples from lesions were streaked on selective media. Three bacterial isolates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, an antibiogram analysis was performed for the three RA strains, using a pattern of 16 common antibiotics to advocate the most effective drugs for a proper treatment. All the RA isolates were sensitive to ceftiofur, sulphamethoxazole-trimethoprim and amoxicillin, whereas all were resistant to gentamicin, tylosin, tetracyclin, colistin sulphate, spectinomycin, lincomycin and oxytetracycline.