Sustainability of food side streams: a case study of fermented blends made with sour whey and sunflower press cake powder using the back-slopping technique

The exploitation of by-products is a key factor to increase the sustainability of the agri-food chain and fermentation is a simple and eco-friendly process for achieving safe and suitable food materials. In this study, we investigated the possibility to manage a spontaneous fermentation of blends made with different proportions of two food side streams (bovine acid whey and sunflower press cake powder) through the application of a back-slopping technique of the mixed material incubated at 26°C in static conditions. A full-factorial 2-factor 3-level design of experiment was applied to infer the effect of the percent (w/w) of press cake powder in the mixture (20, 25, and 30%) and the rate of back-slopping inoculum (15, 30, and 45%). The pH value, titratable acidity, content of sugars, organic acids, and phenolic acids, enumeration of lactic acid bacteria, yeasts and molds, bacterial contaminants, presumptive Bacillus cereus, and Escherichia coli were measured for each fermentation step at 0, 24, 48, and 72 h. On the same samples, a metataxonomics analysis, targeted on bacterial 16S rRNA gene and fungal ITS region, was performed by using the Illumina MiSeq platform. Acidification of the blends (on average, starting pH = 5.45 ± 011, final pH = 4.61 ± 0.11; starting acidity =13.68 ± 1.02 °SH/50 mL, final acidity = 28.17 ± 2.92°SH/50 mL) and high LAB counts (on average, 9.39 log CFU/g ± 0.25) were observed at the end of each refreshment. In all fermented mixtures, B. cereus, E. coli, and molds counts were lower than the detection limit (<2 log CFU/g), whereas bacterial contaminants, overall spore-formers, were always present (3.74 log CFU/g ± 0.27). After 72 h, the dropping of pH value was maximum, yielding significant differences compared to previous fermentation steps (p < 0.01); particularly, the lowest pH (4.45 ± 0.06) was achieved in the central points of DoE (25% of press cake powder and 30% of back-slopping rate), representing the most suitable condition. Results from both culture-dependent and -independent techniques were consistent; although Lactococcus lactis, continuously deriving from the acid whey, was the main LAB, Pediococcus pentosaceus appeared and, in some cases, became the dominant species. Finally, a long-term trial (about 1 month), using the best condition previously pointed out, was performed with an extension of the incubation time to 84 h for each refreshment. The increase in acidity forced the natural selection toward acid-tolerant microbial strains confirming the former results. Although preliminary, these findings can be useful for developing innovative operations to manage these two relevant side streams implementing the circularity of food resources

Lactic and propionic acid bacteria starter cultures for improved nutritional properties of pea, faba bean and lentil

Increasing plant-based food consumption as a sustainable and health-oriented alternative to meat is pivotal. Pulses are rich in proteins, minerals, and vitamins; however, they also contain antinutritional compounds, impairing their nutritional value. This study addresses this challenge through the development and application of four distinct microbial consortia in pulse-based fermentations, featuring lactic acid bacteria or a combination of lactic and propionic acid bacteria. Microbial starters significantly reduced galacto-oligosaccharides in all pulse materials, concurrently degrading vicine and convicine in faba beans, while the impact on tannins in faba beans and lentil was moderate. Fermentation with lactic acid and propionic acid bacteria consortia exhibited notable vitamin B12 production, and the effect on the content of phenolic compounds of the studied pulses was also evidenced. Additionally, genomic analyses discerned distinctive profiles among the samples, elucidating the microbial community dynamics shaping fermentation outcomes. The results of this study proved how fermentation can advance the development of pulse-based products with improved nutritional and sustainability attributes

Application of a novel amplicon-based sequencing approach reveals the diversity of the Bacillus cereus group in stored raw and pasteurized milk

Members of the Bacillus cereus sensu lato (B. cereus group) are spore-forming organisms commonly associated with spoilage of milk and dairy products. Previous studies have shown, by using 16S marker gene sequencing, that the genus Bacillus is part of the core microbiota of raw bovine milk and that some members of this genus is able to grow during sub-optimal storage (8 °C) of pasteurized consumption milk. Here, the composition of this genus in pasteurized consumption milk samples, collected from two dairies, over a one-year period and stored at 4 or 8 °C up to the end of shelf life is uncovered. Our results show that the B. cereus group is the dominant Bacillus group in stored consumption milk. By applying a new marker gene sequencing approach, several dominating phylogenetic clusters were identified within the B. cereus group populations from the milk samples. There was a higher phylogenetic diversity among bacteria from milk stored at 8 °C compared to milk stored at 4 °C. Sampling period and the dairy the samples were collected from, also significantly influenced the diversity, which shows that the B. cereus group population in consumption milk is heterogeneous and subjected to temporal and spatial changes. The new approach applied in this study will facilitate the identification of isolates within the B. cereus group, of which some are potential spoilage bacteria and pathogenic contaminants of milk and dairy products.acceptedVersio

Dynamics of starter, adjunct non-starter lactic acid bacteria and propionic acid bacteria in low-fat and full-fat Dutch-type cheese

The microbial dynamics of Dutch-type cheeses differing in starter (commercial DL starter or single strain of Lactococcus lactis ssp. cremoris), adjunct (Lactobacillus or Propionibacterium) and fat contents (10% or 28% fat) were investigated by culture-dependent and culture-independent analysis. The cheese microbiota was dominated by the adjunct Lactobacillus after 4 weeks of ripening and the fat content did not influence the microbial diversity. The Leuconostoc sp., presumably from the DL starter, was detected in cheeses made with added Lactobacillus plantarum and Lactobacillus rhamnosus and was not detected in cheese made with added Lactobacillus paracasei after 4 and 7 weeks. No Lactobacillus spp. were detected in cheese with added Propionibacterium, while Leuconostoc was the only species detected. In cheeses made with Lc. lactis ssp. cremoris as starter, the Lactobacillus microbiota was similar to the cheese milk microbiota after 24 h while after 4 weeks different species of Lactobacillus and Leuconostoc were detected.acceptedVersio

Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond

publishedVersio

Application of a novel amplicon-based sequencing approach reveals the diversity of the Bacillus cereus group in stored raw and pasteurized milk

Members of the Bacillus cereus sensu lato (B. cereus group) are spore-forming organisms commonly associated with spoilage of milk and dairy products. Previous studies have shown, by using 16S marker gene sequencing, that the genus Bacillus is part of the core microbiota of raw bovine milk and that some members of this genus is able to grow during sub-optimal storage (8 °C) of pasteurized consumption milk. Here, the composition of this genus in pasteurized consumption milk samples, collected from two dairies, over a one-year period and stored at 4 or 8 °C up to the end of shelf life is uncovered. Our results show that the B. cereus group is the dominant Bacillus group in stored consumption milk. By applying a new marker gene sequencing approach, several dominating phylogenetic clusters were identified within the B. cereus group populations from the milk samples. There was a higher phylogenetic diversity among bacteria from milk stored at 8 °C compared to milk stored at 4 °C. Sampling period and the dairy the samples were collected from, also significantly influenced the diversity, which shows that the B. cereus group population in consumption milk is heterogeneous and subjected to temporal and spatial changes. The new approach applied in this study will facilitate the identification of isolates within the B. cereus group, of which some are potential spoilage bacteria and pathogenic contaminants of milk and dairy products

Metataxonomic analysis and host proteome response in dairy cows with high and low somatic cell count: a quarter level investigation

Abstract Host response to invasive microbes in the bovine udder has an important role on the animal health and is essential to the dairy industry to ensure production of high-quality milk and reduce the mastitis incidence. To better understand the biology behind these host-microbiome interactions, we investigated the somatic cell proteomes at quarter level for four cows (collected before and after milking) using a shotgun proteomics approach. Simultaneously, we identified the quarter microbiota by amplicon sequencing to detect presence of mastitis pathogens or other commensal taxa. In total, 32 quarter milk samples were analyzed divided in two groups depending on the somatic cell count (SCC). The high SCC group (>100,000 cell/mL) included 10 samples and significant different proteome profiles were detected. Differential abundance analysis uncovers a specific expression pattern in high SCC samples revealing pathways involved in immune responses such as inflammation, activation of the complement system, migration of immune cells, and tight junctions. Interestingly, different proteome profiles were also identified in quarter samples containing one of the two mastitis pathogens, Staphylococcus aureus and Streptococcus uberis, indicating a different response of the host depending on the pathogen. Weighted correlation network analysis identified three modules of co-expressed proteins which were correlated with the SCC in the quarters. These modules contained proteins assigned to different aspects of the immune response, but also amino sugar and nucleotide sugar metabolism, and biosynthesis of amino acids. The results of this study provide deeper insights on how the proteome expression changes at quarter level in naturally infected cows and pinpoint potential interactions and important biological functions during host-microbe interaction

High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples

Abstract Background Classification of pathogenic Escherichia coli (E. coli) has traditionally relied on detecting specific virulence associated genes (VAGs) or combinations thereof. For E. coli isolated from faecal samples, the presence of specific genes associated with different intestinal pathogenic pathovars will determine their classification and further course of action. However, the E. coli genome is not a static entity, and hybrid strains are emerging that cross the pathovar definitions. Hybrid strains may show gene contents previously associated with several distinct pathovars making the correct diagnostic classification difficult. We extended the analysis of routinely submitted faecal isolates to include known virulence associated genes that are usually not examined in faecal isolates to detect the frequency of possible hybrid strains. Methods From September 2012 to February 2013, 168 faecal isolates of E. coli routinely submitted to the Norwegian Institute of Public Health (NIPH) from clinical microbiological laboratories throughout Norway were analysed for 33 VAGs using multiplex-PCR, including factors associated with extraintestinal pathogenic E. coli (ExPEC) strains. The strains were further typed by Multiple Locus Variable-Number Tandem-Repeat Analysis (MLVA), and the phylogenetic grouping was determined. One isolate from the study was selected for whole genome sequencing (WGS) with a combination of Oxford Nanopore’s MinION and Illumina’s MiSeq. Results The analysis showed a surprisingly high number of strains carrying ExPEC associated VAGs and strains carrying a combination of both intestinal pathogenic E. coli (IPEC) and ExPEC VAGs. In particular, 93.5% (101/108) of isolates classified as belonging to an IPEC pathovar additionally carried ExPEC VAGs. WGS analysis of a selected hybrid strain revealed that it could, with present classification criteria, be classified as belonging to all of the Enteropathogenic Escherichia coli (EPEC), Uropathogenic Escherichia coli (UPEC), Neonatal meningitis Escherichia coli (NMEC) and Avian pathogenic Escherichia coli (APEC) pathovars. Conclusion Hybrid ExPEC/IPEC E. coli strains were found at a very high frequency in faecal samples and were in fact the predominant species present. A sequenced hybrid isolate was confirmed to be a cross-pathovar strain possessing recognised hallmarks of several pathovars, and a genome heavily influenced by horizontal gene transfer