PCR-DGGE markers for qualitative profiling of microbiota in raw milk and ripened cheeses

Microbiological Biodiversity of Regional Cow, Goat and Ewe Milk Cheeses Produced in Poland and Antibiotic Resistance of Lactic Acid Bacteria Isolated from Them

(1) Unique sensory values of traditional and regional dairy products made them more and more popular among consumers. Lactic acid bacteria naturally occurring in these products can express antibiotic resistance and be a reservoir of antibiotic resistance genes (ARG) in the environment. The aim of the study was to characterize the microbial diversity of twenty regional cheeses produced from non-pasteurized cow, goat and ewe milk, and investigate the phenotypic and genotypic antibiotic resistance (AR) of lactic acid bacteria isolated from these products. (2) Conventional microbiological methods were applied for the enumeration of lactic acid bacteria (lactobacilli and lactococci) and their isolation, and for the enumeration of Enterococcus, Staphylococcus, Enterobacteriaceae and spores. The disc diffusion method was applied for phenotypic AR. The PCR-based methods were used for strain identification, microbiological diversity of cheeses (PCR-DGGE), and for AR gene detection. (3) Among 79 LAB isolates the most frequent species were L. plantarum (n = 18), Leuc. lactis (n = 17), Lc. lactis (n = 11), Leuc. mesenteroides (n = 9) and L. pentosus (n = 8). Additionally, by using the PCR-DGGE method, DNA of L. casei was found in nine products. Lactobacilli (5.63-8.46 log cfu/g) and lactococci (6.15-8.41 log cfu/g) predominated over Enterococcus (max. 4.89 log cfu/g), Staphylococcus (max. 4.18 log cfu/g), and Enterobacteriaceae (mostly up to 4.88 log cfu/g). Analysis of phenotypic resistance to tetracycline (30 µg), erythromycin (15 µg), and chloramphenicol (30 µg) showed that 29% of LAB isolates were resistant to one antibiotic, 8%-to two, and 12%-to all tested antibiotics. Antibiotic resistance genes (AGR) for tetracycline (tet(M), tet(L), tet(W)), erythromycin (erm(B)) and chloramphenicol (cat-TC) were detected in 30 (38%), 29 (36.7%) and 33 (43.4%) LAB isolates, respectively. Among 31 LAB isolates phenotypically susceptible to all tested antibiotics, only 5 (16%) had no ARGs. (4) The results obtained in our work shed light on the potential threat posed by the widespread presence of ARGs in LAB present in regional cheeses.

Genomic and Metabolic Features of an Unexpectedly Predominant, Thermophilic, Assistant Starter Microorganism, Thermus thermophilus, in Chinese Inner Mongolian Cheese

Inner Mongolian cheese is a traditional dairy product in China. It is produced without rennet, using naturally acidified milk that is simmered to achieve whey separation. In order to analyse the impact of simmering on the microbial community structure, high-throughput sequencing was performed to obtain bacterial 16S rRNA sequences from cheeses from the Ordos (ES), Ulanqab (WS), Horqin (KS) and Xilingol (XS) grasslands of Inner Mongolia. The relative abundance of an unexpected microorganism, Thermus thermophilus, ranged from 2% to 9%, which meant that its dominance was second only to that of lactic acid bacteria (LABs). Genome sequencing and fermentation validation were performed in T. thermophilus N-1 isolated from the Ordos, and it was determined that T. thermophilus N-1 could ingest and metabolise lactose in milk to produce lactate during the simmering process. T. thermophilus N-1 could also produce acetate, propionate, citrate and other organic acids through a unique acetate production pathway and a complete propionate production pathway and TCA cycle, which may affect texture and flavour development in Inner Mongolian cheese. Simultaneously, the large amount of citrate produced by T. thermophilus N-1 provides a necessary carbon source for continuous fermentation by LABs after the simmering step. Therefore, T. thermophilus N-1 contributes to cheese fermentation as a predominant, thermophilic, assistant starter microorganism unique to Chinese Inner Mongolian cheese.

Comparison of microbiota and volatile organic compounds in milk from different sheep breeds

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.

Community-level genetic profiles of actinomycetales in long-term biowaste-amended soils

Actinomycetales is an order of actinobacteria that have an important role in the decomposition of organic matter. Their abundance and distribution can reflect a good level of soil fertility as well as biological activity. In this research study, actinomycetal diversity in soil was investigated under various field treatments with biowastes. Initially, unvegetated agricultural soil plots of 4 m² had been annually amended with increasing rates of municipal solid waste compost (MSWC at 40, 80 and 120 t ha^-1 year^-1) and farmyard manure (FM at 40 and 120 t ha^-1 year^-1) for eight consecutive years. Control consisted of unamended soil and all treatments were distributed in four randomized complete blocks. At the end of the experimental period, total DNA was extracted from fresh topsoil samples (0-20 cm) then nested PCR-DGGE sequencing method was applied to assess the long-term effect of treatments on the diversity of actinomycetes. Analytical outcomes revealed the presence of ten actinomycetal families with Streptomycetaceae, Pseudonocardiaceae and Nocardioidaceae being the most dominant regardless to changes in experimental conditions. Besides, the long-term accumulation of both biowastes in soil affected the diversity of actinomycetal communities in different ways including contribution, stimulation or inhibition. Interestingly, soil treated with MSWC at an equivalent rate of 40 t ha^-1 year^-1 was likely to provide optimal growth conditions for major identified genera because it showed the highest actinomycetal diversity as compared to the rest of the treatments.

Influence of 2,4-D residues on the soil microbial community and growth of tree species

The 2,4-D (2,4-dichlorophenoxyacetic acid) has low half-life in the soil, but it is capable of altering the soil microbial community. The objective of this study was to evaluate the influence of 2,4-D residues on the structure of the soil microbial community and the growth of tree species. The tolerance and phytoremediation potential of tree species were evaluated. The microbial analysis was performed by T-RFLP. The 2,4-D herbicide reduced the plant height of K. lathrophyton, number of leaves of C. ferrea and K. lathrophyton and root dry matter allocation for C. brasiliense, I. striata, P. heptaphyllum, and T. guianensis. Cucumis sativus intoxication on soil contaminated with 2,4-D was not significant. The structure of Fungi community in the rhizospheric soils of C. ferrea was altered. The herbicide 2,4-D increased the diversity of Fungi in rhizospheric soils of P. heptahyllum and R. grandis. Most tree species were tolerant, and the evaluation time was sufficient to remedy 2,4-D. The structures of the microbial communities Archaea, Bacteria, and Fungi were little influenced by 2,4-D. The diversity of the Archaea domain was not affected, the diversity of the Bacteria in Inga striata decreased while the fungi increased in Protium heptaphyllum and Richeria grandis with 2,4-D.

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk

The aim of this study was to define the composition of microbiota and the volatile organic compounds (VOCs) in samples of raw milk collected for 22 months between 2012 and 2014 originated from north-eastern region of Poland. The results revealed that the VOCs profile changed with respect to the season of milk collection, and milk collected in autumn was characterized by a higher content of acetic acid (C2), propionic acid (C3) and valeric acid (C5), whereas spring was characterized by a frequent presence of acetone (Ac), ethanol (Et) and ethyl acetate (EtAc). Bacterial species composition changed considerably within the tested period and some bacterial species/groups occurred seasonally, e.g. L. helveticus (summer), L. casei (winter). The results show usefulness of the applied techniques (PCR-DGGE and HS-GC) and data analysis (PCA, correlation coefficients) methods in characterizing the raw milk quality intended for dairy production.