In this study, we compared the microbiota and volatile organic compounds (VOC) present in the milk obtained from 3 different sheep breeds, namely Merino, Lacaune, and Assaf. Udder milk was collected from 21 animals, 7 from each breed. Bacterial microflora was determined metagenomically by extracting the DNA from the milk and analyzing the V3-V4 region of the 16S rRNA gene. Headspace solid-phase microextraction gas chromatography-mass spectrometry method was used to analyze VOC. The metagenomic analysis revealed (for Merino, Lacaune, and Assaf milk, respectively) Firmicutes (66.32, 69.36, and 57.08%), Actinobacteria (19.09, 7.67, and 19.40%), Proteobacteria (13.76, 21.06, and 22.19%), and Bacteroidetes (0.84, 1.91, and 1.33%) phyla in the milk samples. Lactobacillus was highly abundant in the milk of 3 breeds (29.64, 43.50, and 18.70%). The genera constituting more than 2% of all bacteria in all groups were Jeotgalicoccus (7.19, 5.34, and 10.77%), Enterococcus (5.18, 9.78, and 3.64%), and Corynebacterium (4.08, 3.00, and 13.44%). A total of 32 different VOC were identified by headspace solid-phase microextration analysis with 9, 30, and 24 different compounds from Merino, Lacaune, and Assaf breeds, respectively. Although ketone was the most abundant compound in Merino milk (71.84%), hydrocarbons were the most detected in Lacaune and Assaf milk (37.18% and 55.42%, respectively). A positive correlation was found between acetone, which was detected at the highest level in all groups, with Salinicoccus, Alloiococcus, Psychrobacter, and Dietzia. In addition, a negative correlation was found between the Lactobacillus genus, detected at the highest level in all groups, with methyl cyclopentane, 3-methylheptane, octane, decane, 3,3-dimethyloctane, and dodecane. Thus, differences were observed in the bacterial microflora and VOC in the sheep milk from different breeds under different feeding and breeding conditions.

Dairy products harbor complex and dynamic microbial communities that contribute to their sensory properties, safety, and cultural distinctiveness. Raw milk contains a diverse microbiota shaped by seasonality, storage conditions, lactation stage, animal health, farm management, and genetics, serving as a variable starting point for further processing. Fermentation, whether spontaneous or starter driven, selects for subsets of lactic acid bacteria (LAB), yeasts, and molds, resulting in microbial succession that underpins both artisanal and industrial products such as kefir and cheese. Kefir represents a balanced LAB–yeast symbiosis, with species composition influenced by grain origin, milk type, and processing parameters, whereas the cheese microbiota reflects the interplay of starter and non-starter LAB, coagulants, ripening conditions, and “house microbiota”. Methodological factors—including DNA extraction, sequencing platform, and bioinformatic pipelines—further impact the reported microbial profiles, highlighting the need for standardization across studies. This review synthesizes current knowledge on raw milk, kefir, and cheese microbiomes, emphasizing the biological, technological, environmental, and methodological factors shaping microbial diversity. A holistic understanding of these drivers is essential to preserve product authenticity, ensure safety, and harness microbial resources for innovation in dairy biotechnology.

Background: Laying hens, which are widely utilized for consumption and export in various regions, experience prolonged antibiotic exposure due to their longer lifespan, increasing the risk of antibiotic resistance and impacting the microbial environment of poultry slaughterhouses. Given the significance of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli in food safety, this study aimed to investigate the prevalence of ESBL genes in E. coli isolated from a laying hen slaughterhouse in Konya, Turkey. Methods: Sampling was conducted using a convenient sampling approach, and a total of 150 samples were collected from a single slaughterhouse over six visits during both warm (June–August) and cold (January–March) seasons to evaluate seasonal variations. Samples were categorized into environmental sources (personnel, air, wastewater, eggs) and carcass-related sources (cloaca, carcasses at critical control points, final product). Classical cultural and molecular techniques and antimicrobial susceptibility tests were used for ESBL presence and gene characterization. For sequence analysis, the bidirectional Sanger Gene sequence analysis method was applied. Results: PCR-based detection identified 10 of the 17 isolates as E. coli by amplifying the uspA gene, and bidirectional Sanger sequencing further confirmed these isolates at the species level. The E. coli isolates were detected at various sampling areas, including personnel, carcasses after evisceration, and raw wastewater samples collected at different time points. In the multiplex PCR analysis, most ESBL isolates were positive for the blaCTX-M gene. The co-existence of blaTEM and blaCTX-M genes was detected in five samples. Additionally, three genes (blaSHV, blaCTX-M, and blaOXA) were identified in a carcass sample after evisceration. All ESBL-producing isolates harbored the blaCTX-M1 gene, and multiple antibiotic resistance was observed across all isolates. The presence of these genes was strongly associated with resistance to ampicillin, amoxicillin-clavulanic acid, aztreonam, cefepime, cefpodoxime, cefuroxime, and cephalothin, highlighting the critical role of blaCTX-M in driving the multidrug resistance patterns observed in this study. The highest resistance rate (80%) was observed in “personnel” and “carcass samples after evisceration”, while all isolates remained sensitive to carbapenems (imipenem and meropenem). Conclusions: Our findings highlight the importance of the laying hen slaughter line as a potential source of contamination with ESBL-producing E. coli, which poses significant implications for food safety and public health. These findings underscore the need for improved control measures to mitigate ESBL E. coli transmission in poultry processing and highlight the importance of optimizing antibiotic use strategies in laying hen farming.

Introduction: This study aimed to determine the bacterial diversity of chicken carcasses and their surrounding environment at various stages along a poultry slaughter line. Material and Methods: Amplicon sequencing of the 16S rRNA gene was employed to assess the shifts in bacterial community diversity at both phylum and genus levels. Samples were collected from September to November 2021, targeting carcass surfaces at various operational stages (post-defeathering, post-evisceration, post-water chilling, and post-cooling), as well as from the internal environments and air of these units. The study took place in a vertically integrated poultry slaughterhouse in Konya, Turkey. Results: Microbial diversity increased after the chilling and storage stages as a result of redistribution of the microorganisms after the physical effect of the slaughtering stages. The final product sample taken after storage had the highest bacterial abundance. The abundance at this stage was found to be strongly correlated with that at other slaughtering stages, as well as with the abundance in chilling water and on the personnel’s hands. The common genera in chicken carcasses during slaughter stages were Macrococcus, Acinetobacter, Enterococcus, Escherichia-Shigella, Psychrobacter, Streptococcus, Lactococcus and Ligilactobacillus. Microbiome data in environmental samples indicated that the genera in highest relative abundance were Bacillus, Anoxybacillus, Acinetobacter and Psychrobacter. In air samples, the storage room had the highest diversity and in this place Bacillus spp. and Staphylococcus spp. were in the majority. Conclusion: This study may provide some useful information to pinpoint the critical contamination sources in the poultry slaughtering process.