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.

Süt ve süt ürünleri içerdikleri yüksek besin değeriyle günlük diyetin önemli bir parçasını oluşturmaktadır. Ancak bu önemli özelliklerinin yanı sıra en fazla hile yapılan gıdalar arasında yer almaktadır. Koyun-keçi sütü ve ürünlerine inek sütünün karıştırılması süt ve süt ürünlerinde en sık karşılaşılan hilelerin başında gelmektedir. Bu durum, tüketiciler tarafından tercih edilmeyen sosyo-ekonomik potansiyel risklere neden olmaktadır. Bu çalışmada koyun ve keçi sütlerine farklı oranlarda karıştırılan inek sütü miktarının TaqMan Real-Time PCR ile tespit edilmesi amaçlanmıştır. Bu amaçla %1, %5, %10, %25, %75 ve %90 oranlarında keçi ve koyun sütlerine inek sütü karıştırılmıştır. Ayrıca saf inek sütünden elde edilen DNA sulandırılarak PCR işleminin duyarlılığı araştırılmıştır. Bu çalışmanın sonucunda, koyun ve keçi sütlerine karıştırılan %1 inek sütü ve 0,003 ng DNA varlığı tespit edilmiştir. Araştırma sonucunda TaqMan Real-Time PCR’ın koyun ve keçi sütlerine karıştırılan düşük düzeydeki inek sütünün tespit edilmesinde güvenilir ve hassas bir yöntem olarak kullanılabileceği düşünülmektedir.

Background: The emergence of extended-spectrum β-lactamase (ESBL) producing and colistin-resistant Escherichia coli in retail meat poses a significant public health risk. Method: A total of 180 retail meat samples (chicken parts, internals, processed products; lamb; beef; fish) were purchased from markets and butcher shops across Turkiye. Presumptive ESBL-producing isolates were screened on chromogenic agar and phenotypically confirmed. Species identity was verified by uspA PCR, and resistance genes (blaCTX-M, blaTEM, blaOXA, blaSHV, mcr-1, mcr-2, mcr-3) were analyzed. Colistin MICs were determined by broth microdilution, while antimicrobial susceptibility of ESBL-positive isolates was assessed by disk diffusion. Results: Overall, ESBL-producing E. coli were detected in 21.7% (n = 39) of the 180 meat samples analyzed, with the highest prevalence observed in chicken parts (26/40, 65.0%) and giblets (6/10, 60%). All ESBL-E. coli isolates harbored blaCTX-M, with blaCTX-M-1 identified as the sole variant. The blaTEM gene was detected in 61.5% (24/39) of ESBL-positive E. coli isolates. Colistin resistance was identified in six isolates (15.4%), all of which carried the mcr-1 gene. Additionally, one lamb minced meat isolate harbored the mcr-2 gene. Co-occurrence analysis revealed that the most frequent resistance gene combination among ESBL-producing isolates was blaCTX-M1 + blaTEM, detected predominantly in chicken meat samples, while mcr-1 was observed only in isolates harboring single or limited resistance genes, suggesting a distinct acquisition pattern. Conclusions: A high prevalence of blaCTX-M-1 and the co-occurrence of mcr genes were detected in E. coli isolates from retail meat, particularly poultry. The detection of mcr-1/mcr-2 co-carriage in lamb meat, though rare, highlights the need for broader surveillance. These findings underscore the need for integrated monitoring and prudent antimicrobial use in food animals. The use of antibiotics as growth promoters is prohibited in Türkiye, and therapeutic applications require a veterinary prescription; however, stronger enforcement remains essential to limit the dissemination of multidrug-resistant bacteria in the food chain.

This study was carried out on the effect of different amounts of whey on the kefir production process and the bacterial microbiota of the beverages. Fermentation was carried out by mixing commercial kefir grains with cow, sheep, and goat milk with their whey at concentrations of 0% (control group), 25%, 50%, and 75%. The bacterial microbiota in the produced beverages and the relative abundances of seven microorganisms (Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus delbrueckii, Lactococcus lactis, Streptococcus thermophilus, Leuconostoc mesenteroides, and acetic acid bacteria) were determined using metagenomic analysis targeting the V3-V4 region of 16 S rRNA gene, and quantitative polymerase chain reaction (qPCR), respectively. Lactococcus lactis and Leuconostoc mesenteroides were detected in higher abundance in whey-containing goat samples. While Lactobacillus was dominant in the cow milk samples containing 0%, 25%, and 50% whey, Enterococcus was dominant in the samples containing 75% whey. In sheep milk samples, Lactobacillus was dominant in samples with 75% and 50% whey, Lactococcus was dominant in samples with 25% whey, and Enterococcus was dominant in samples with no (0%) whey. Lactobacillus was dominant in all goat milk samples. In conclusion, high levels of lactic acid bacteria were shown to preserve their viability in the experimentally produced beverages with the addition of whey at different concentrations, and the whey could be used to produce kefir.