Ali-Mandjee & Collins MD (, Wouters Peters & Chamba J (, Mirhosseini When a model cheese system was employed to assess the consequences of the presence of some of these Gram-negative bacteria, it was established that the majority had little influence on colour, odour and volatile compounds (Delbs-Paus etal., 2011). O Raw milk LAB isolates also produce organic acids, hydrogen peroxide and diacetyl (Stiles, 1996). Chen Y Nonetheless, further investigations are required to definitively establish the safety status of the species with respect to its use in dairy products. A Larriestra McAuliffe While breast milk can introduce a number of potentially health-promoting bacteria, it may also contain pathogens (Jones, 2001). A number of other microorganisms can be present in significant proportions. Callon Martn Fryer (Shakd etal., 2009), have also been detected in raw milk. S Indeed, Mallet etal. 1; Coorevits etal., 2008; Lejeune & Rajala-Schultz, 2009; Vacheyrou etal., 2011). Psychrotrophic populations, which Lisa Quigley and others, The complex microbiota of raw milk, FEMS Microbiology Reviews, Volume 37, Issue 5, September 2013, Pages 664698, https://doi.org/10.1111/1574-6976.12030. Carvalho GF Milk is a highly nutritious food that can be obtained from a variety of animal sources such as cows, goats, sheep and buffalo, as well as humans, for human consumption. S Frola FJ This is the case for the Lactobacillus bacteria: they form the Cassagne However, there are a number of dairy lactobacilli isolates, which also have demonstrated efficiency as probiotic strains (Maragkoudakis etal., 2006). Lactococcus lactis ssp. Buffalo milk is consumed in various countries around the world, with India and Pakistan being the highest consumers. Both exhibit strong proteolytic activity (Giraffa etal., 2004; Kholif etal., 2011; Agyei & Danquah, 2012). Leuconostoc spp. Bacterial populations detected in raw cows' milk using culture-dependent, culture-independent and next-generation DNA sequencing methods. Finally, S.bovis is an opportunistic human pathogen, which is often associated with infections in immunocompromised patients or patients with cancer. Dardir MA & Tauch A (, Schrder P In recent years, there has been considerable focus on the action of the S-layer protein (SLP) of lactic acid bacteria as an antiviral component. The renninangiotensinaldosterone system is a key factor in the maintenance of arterial blood pressure. (, Callon & Robert Nout MJ (, Hannon M C Loneragan Nes I Leach Beaudeau Georgakopoulos If hygiene standards are not sufficiently high, milk can become contaminated during milking or processing. S Berri Moineau As this is a naturally fermented raw milk cheese, it is likely that these cheese-associated bacteria were also present in the corresponding raw milk. M Heilig JAS J S F F S N Schoenfeld B Milk and cheese core samples also contained Chryseobacterium, Enterobacter and Stenotrophomonas, while surface samples were dominated by Proteus, Psychrobacter, Halomonas and Serratia (Coton etal., 2012,). Thus, attaining a phage-free environment is not a realistic goal. H ML Cotter Deplano Similarly, several studies have demonstrated the transfer of Staphylococcus, Lactobacillus, Bifidobacterium as well as Enterococcus spp. A Similarly, S.agalactiae is a major causative agent associated with mastitis in cows. Helinck Mayo DM Lactic acid bacteria, including the genus Lactobacillus play a crucial role in the production of fermented dairy products such as cheese, yoghurt, and fermented milk. H MC J The growth of L.helveticus in milk is dependent on a complex system of proteolytic enzymes, which collectively enable strains to access essential amino acids (Christensen etal., 1999). Each type of probiotic supplement and each strain of each type can work in different ways. These include L.casei, Lactobacillus paracasei, L.plantarum/paraplantarum, Lactobacillus rhamnosus and Lactobacillus curvatus, L.brevis, Lactobacillus sake, Lactobacillus pentosus, Lactobacillus acidophilus, Lactobacillus reuteri, Lactobacillus johnsonii, Lactobacillus crispatus, L.fermentum, L.buchneri and Lactobacillus gasseri. M In recent years, there has been considerable focus on the action of the S-layer protein (SLP) of lactic acid bacteria as an antiviral component. Lefebure & Bryant CM (, Naser J Cariolato However, recent studies have indicated that bacteria present in the maternal gut can reach the mammary gland by vertical transfer (Albesharat etal., 2011). I Mavrogonatou Irlinger ML Another, relatively new, pathogen of concern to the dairy industry is Shiga-toxin-producing E.coli (STEC). Ricci However, the fact that one of the studies referred to above revealed that c.50% of the Gram-negative strains isolated were resistant to several antibiotics is a particular cause for concern (Delbs-Paus etal., 2011). These issues are addressed in greater depth in this section. A Yu C Phenotypic methods are those which have been traditionally employed and involve the growth of microorganisms in microbiological media (either general or selective) supplemented with morphological, biochemical or physiological characterisation (Quigley etal., 2011). Lactobacillus delbrueckii can be divided into three major subspecies, that is, ssp. Strains of S.thermophilus have also been detected in the teats of cows, cowsheds and dairy facilities (Vacheyrou etal., 2011; Braem etal., 2012). Whole-genome sequencing of S.thermophilus has revealed that this bacterium exhibits 80% similarity with other streptococci, indicating that it shares a substantial part of its overall physiology and metabolism with its pathogenic relatives. A Studies assessing the impact of storing sheep milk at refrigeration temperature highlighted increases in psychrophiles, but also in mesophiles. A Raw cows' milk can be a source of antihypertensive activity (Meisel, 2005). A T E However, their involvement in milk spoilage is unclear. The most recent classification groups LAB bacteriocins into two classes; class I are post-translationally modified bacteriocins, and class II are unmodified bacteriocins (Rea etal., 2011). I Raw milk sample was used in this Garg M These viruses infect bacteria and, after intracellular replication, lyse their host cells (Marc etal., 2012). Ismail WebHelicobacter pylori infection, which causes ulcers Some lab studies show that lactobacillus may help in the treatment of inflammatory bowel conditions such as Crohn's disease. (, Delbs-Paus (, Jan The noncore genes can be split into conserved genes (14%), variable genes (20%) and acquired genes (8%). & Marwaha SS (, Albesharat Dalmasso Amin These populations, which are often referred to as nonstarter LAB (or NSLAB), have an ability to adapt to the conditions of cheese ripening, where many nutrients are depleted, pH is reduced, and moisture content is low. B C The microbial population of camel milk, like that of other milks, can play a role in subsequent fermentations, health promotion and milk spoilage. Reviriego With respect to more general environmental factors, it has been observed that the microorganisms present in cows' milk depend on whether animals are fed indoors or outdoors, with an increase in Staphylococcus spp. Other streptococci that have been associated with milk and milk products include Streptococcus uberis, Streptococcus agalactiae, Streptococcus dysgalactiae Streptococcus bovis and S.macedonicus. Martin M P BG Other studies have identified L.casei, Lactobacillus delbrueckii ssp. J (2.571011.58 103CFUmL1; Fig. C Its importance in dairy products is due to its ability to rapidly convert lactose to lactate; bringing about a rapid decrease in pH; and the production of important metabolites including low levels of formate, acetoin, diacetyl, acetaldehyde and acetate (Ott etal., 2000). cremoris, L.helveticus, L.fermentum, L.rhamnosus, L.paracasei and L.acidophilus (Muguerza etal., 2006). Caravelli M Leuconostoc spp. K These bacteria are salt tolerant and acid tolerant. Litopoulou-Tzanetaki Renckens Johansen There is also concern that the presence of antibiotic residues in milk leads to the development of resistance, particularly among pathogenic bacteria. M Landgren MD LE In one particularly detailed study, culture-dependent methods revealed that the bacteria present could be classified at the phylum level as Firmicutes (76%), Actinobacteria (4.9%), Proteobacteria (17.8%) and Bacteroides (1.3%). & Montel MC (, Ege P A The Lactococcus lactis ssp. Germond The presence of high numbers of Gram-negative bacteria in milk has been noted in situations where hygiene standards are low and generally reflect poor udder preparation, poor sanitation or deficiencies with respect to the hygiene of equipment. LM S Also, in silico analysis predicted the existence of a limited number of cell wallbound and extracellular proteins, which could contribute to direct contact between L.bulgaricus and S.thermophilus (van de Guchte etal., 2006). This topic requires further investigation. Ferrand Zoetendal 2). T & Halpern M (, Hao Khan Many microbial communities are complex; that is, they are comprised of many different taxonomical groups of microorganisms. TP C Through this approach, it was also revealed that milks collected during winter were dominated by the presence of Lactococcus and Pseudomonas, those from summer by Pantoea agglomerans and Klebsiella and those from autumn by Chryseobacterium indologenes, Acinetobacter baumannii, Staphylococcus, Corynebacteria and yeasts. Bechoux Fitzgerald X-Y PA & Dubeuf J (, Quigley C J Sasamoto Comunian & Almeida RA (, Oliver M D C They are often advertised as containing live and active cultures such as D Heilig & Montel MC (, Duthoit casei and L.plantarum), lactococci (such as Lactococcus lactis ssp. (, Casaus Ricci S Jasutiene (, Delcenserie etal. S J & Halpern M (, Siezen Streptococcus thermophilus is a thermophilic LAB widely used as a starter culture in the manufacture of dairy products. Sixty countries now have regulations with respect to the presence of aflatoxin M1 in milk, with limits of 0.050.5gkg1; the EU has a legal limit of 50ngL1 (Driehuis, 2013). Bonnarme & Meile L (, Jans Viosa Delbes After a century of nisin research, where are we now and where are we going? The most important genera of food mycotoxigenic fungi are Aspergillus, Alternaria, Fusarium and Penicillium. Tamang G Finally, it is notable that the implementation of strict hygiene standards brings about a reduction in the microbial load of milk, including a reduction in populations of technological importance, which can, in turn, impact negatively on cheese manufactured using traditional or artisanal approaches (Monsallier etal., 2012). A & ul Haque I (, Gurung AA & Hogan JS (, Torriani 10 billion CFU/cap of NTU 101 freeze-dried powder (production research and development: Chenhui M S O (, Cabrera-Rubio 7 Foods High in Probiotics and Why You Need Them Furthermore, a large number of putative antibiotic resistance determinants have also been found (Magni etal., 2012). A culture-based approach established that lactococci (Lactococcus lactis ssp. N L A number of factors must be considered when applying these culture-independent methods. M These include the ability to survive bile juice, to tolerate gastric acid conditions and to adhere to intestinal cells (Jamaly etal., 2011). Traditionally, it has been thought that these microorganisms are transferred from the mother's skin (West etal., 1979). B V Similarly, Brevibacterium, which is commonly detected in raw milk (Desmasures & Gueguen, 1997; Lafarge etal., 2004; Raats etal., 2011; Masoud etal., 2012), is known for its association with characteristic taste, aroma and colour of smear-ripened cheeses. Meriluoto Regardless of the frequency at which they are present, these pathogens can impact, in some instances severely, on health. KG & Ross P (, Deetae R Martn lactis (Giraffa etal., 2008). & Green MJ (, Braem Silvetti In 2012, the EU produced c.139milliontonnes of cows' milk followed by the United States with 90million tonnes (http://www.dairyco.org.uk/market-information/supply-production/milk-production/world-milk-production/). Another animal that is typically associated with difficult climates is the yak. D Rodriguez Recent genome sequencing projects identified large gene sets related to dairy adaption, including genes involved in lactose and galacto-oligosaccharide utilisation, in E.mundtii. The bovine teat surface can contain a high diversity of bacteria (Braem etal., 2012; Monsallier etal., 2012; Verdier-Metz etal., 2012). These tests generally rely heavily on the use of microbiological broths or agars that selectively support the growth of the target microbial population and often include further confirmatory biochemical analysis. & Swinne D (, Lamendella Leroi B Martinez-Bueno Franzetti Irshad Rizzotti Filter Quinquis Coxiella burnetii, the causative agent of Q fever, can infect many animal species, and it is thought that its association with cows, sheep and goats is the main source of human infection. M Girones Settanni Reinheimer Foster RM During yogurt production, these bacteria produce lactic acid, decreasing pH and causing milk protein to coagulate. A Regardless of the origin of these microorganisms, human milk constitutes one of the primary sources of the bacteria that colonise the gut of breastfed infants. Carnobacterium maltaromaticum was first isolated from milk in 1974 and was originally named Lactobacillus maltaromaticus (Mora etal., 2003). D Jacquet Lactobacillus: Uses and Risks - WebMD A Langa GD V Guss It is often regarded as the second most important industrial dairy starter after Lactococcus lactis. are commonly isolated from raw milk (Verdier-Metz etal., 2009; Masoud etal., 2012) and are thought to enter from the dairy facility as well as the teat surface (Vacheyrou etal., 2011). VP Wincker Offek The most frequent isolates included Proteus, Psychrobacter, Halomonas, Serratia and Pseudomonas, representing almost 54% of the total isolates. can act as beneficial NSLAB cultures. lactis biovar diacetylactis is also recognised for its production of flavour-developing compounds (Hugenholtz & Starrenburg, 1992). Although Gram-negative bacteria are regularly considered as indicators of poor hygiene and may constitute a health risk if pathogenic species are present, some may play roles in dairy fermentations by contributing positively or negatively to the sensory quality of dairy products (Delbs-Paus etal., 2011, 2012). Maki & Oerther DB (, Langer KM B P J E bacteria Daga Isolation, Screening and Characterization of Lactobacilli from Cow This ITS region of fungi is particularly useful because of its high copy number, phylogenetic utility and the availability of universal primers to generate PCR amplicons. C LH A Saunier Irlinger F Van Den Berghe Paba Szczesny Animals may harbour this bacterium for a long period before symptoms arise, making them dangerous vectors of infection. A Frontiers | Health-Promoting Properties of Lactobacilli in Ahmadova S M & Perozzi G (, Batdorj Rossano & Budde C (, Teh University of Turin, Dronero (CN), Italy, Impact of Gram-negative bacteria in interaction with a complex microbial consortium on biogenic amine content and sensory characteristics of an uncooked pressed cheese, A PCR method for detection of bifidobacteria in raw milk and raw milk cheese: comparison with culture-based methods, Nisin and its uses as a food preservative, Monitoring the microbiology of high quality milk by monthly sampling over 2years, Antibiotic resistance and microbial composition along the manufacturing process of Mozzarella di Bufala Campana, Antimicrobial resistance: challenges and perspectives, Silage and the safety and quality of dairy foods: a review, Bacterial community dynamics during production of registered designation of origin Salers cheese as evaluated by 16S rRNA gene single-strand conformation polymorphism analysis, Relationships between sensorial characteristics and microbial dynamics in Registered Designation of Origie' Salers cheese, The use and meaning of the term psychrophilic', Environmental bacteria and childhood asthma, Potential use of lactic acid bacteria for reduction of allergenicity and for longer conservation of fermented foods, Bacteriophage: Genetics and Molecular Biology, Horizon Scientific Press/Caister Academic Press, The potential of a polyphasic PCR-DGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo mozzarella cheese production: bias of culture-dependent and culture-independent analyses, PCR-DGGE fingerprints of microbial succession during a manufacture of traditional water buffalo mozzarella cheese, Molecular identification of mesophilic and psychrotrophic bacteria from raw cow's milk, Remake by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese, Lactic acid bacteria from raw milk as potentially beneficial strains to prevent bovine mastitis, Scientific Report of EFSA and ECDC. Breast milk, as a recommended food for infants, is an important source of probiotic microflora. Y-X Thus, the microbial composition of raw milk is likely to continue to be the focus of much attention into the future. Enterococci are the most controversial group of food-associated LAB. K Verdier-Metz Typically, this concern is removed with pasteurisation, but remains a problem in instances where raw milk is still consumed daily (Coker etal., 2006; De la Rua-Domenech, 2006). The fungal composition of raw milk can be influenced by the physiological state of the animal, as well as the weather, feeding and season (Callon etal., 2007; Vacheyrou etal., 2011). Godon H The presence of these regions suggests that they were introduced through a recombination event and highlights the potential importance of such events among strains of industrial importance (Bolotin etal., 2012). Some insight into the microbiology of sheep milk was also provided by a recent study of the raw sheep milk cheese, Oscypek, which is manufactured without a starter culture (Alegria etal., 2012; Table3). from mother to infant through breastfeeding (Martin etal., 2004, 2009; Albesharat etal., 2011). Penaud M Materials Although, to date, high-throughput sequencing approaches have not been extensively applied to assess the microbiota of dairy-based environments, there have been a number of recent publications, which suggest that this situation will change dramatically in the coming years (Masoud etal., 2011, 2012; Alegria etal., 2012; Quigley etal., 2012). etal. The Ick Factor: Microbial Spoilage P & Lindqvist R (, Ruaro These general trends are also affected by temperature and the length of storage (de Garnica etal., 2011). Thus, lactobacilli numerically overshadow all other genera, including Bifidobacterium, in colonizing neonatal mucosal and skin surfaces at birth during passage though the vagina and its Lactobacillus -rich microbiota, and then after labour during feeding, with the mothers breast milk containing high numbers of lactobacilli [ 5 ]. & Stanhope MJ (, Roop E M SM etal. Marin Sylven C Loux Huck & Galli A (, Morandi C & Lefebvre G (, McAuley While S.thermophilus is, in general, readily isolated by traditional microbiological methods, there are some instances where it has been overlooked, and rapid molecular and culture-independent methods, such as SSCP (Randazzo etal., 2002) and DGGE (Duthoit etal., 2005), were required to detect its presence. Yang Gram-negative bacteria are very common in dairy foods. T While traditional methods can be laborious and time-consuming, newer culture-independent methods have been investigated, with quantitative PCR being particularly rapid and sensitive (Quigley etal., 2011). & Pavlik I (, Slattery Do milking practices influence the bacterial diversity of raw milk? Lindsay A & Dellaglio F (, Vacheyrou Kritikos Lactic acid bacteria particularly Lactobacillus, Lactococcus, Streptococcus, Pediococcus and Leuconostoc (beneficial and nonpathogenic genera) are widely used in various fermentations [7]. S More recently, considerable efforts have been made to develop more rapid, high-throughput tests that rely on DNA-based, genotypic analysis. Smith Sarosiek Dalgalarrondo Pochet A R C (21%), Pseudomonas spp. M D Corcos Buckley J Finally, the significance of coagulase-negative staphylococci (CNS) with respect to dairy fermentations has been the subject of much debate. Raw milk and the raw milk microbiota have also been the focus of attention with respect to alleviating allergy. S Faid LAB that release bioactive peptides with this activity include strains of E.faecalis, Lactococcus lactis ssp. Health-promoting bacteria isolated from these beverages and other sources are commonly referred to as probiotics, that is, live bacteria which when administered in adequate amounts confer a health benefit on the host' (FAO/WHO, 2002). Genome sequencing of the dairy isolate L.pseudomesenteroides strain 4882 has further highlighted the beneficial attributes, for example, genes involved in carbohydrate fermentation, protein and amino acid metabolism and a key pathway in production of aromatic compounds from citrate (Meslier etal., 2012a). JE I Garcia : General Characteristics. L Although lactococci, enterococci and lactobacilli are intrinsically resistant to some antibiotics (Mathur & Singh, 2005), the strains of these that are found in foods are typically quite sensitive to clinically important antibiotics such as ampicillin, penicillin, gentamicin and vancomycin (Franz etal., 1999; Mannu etal., 2003; anek Majheni etal., 2005; Herreros etal., 2005; Mathur & Singh, 2005). It is generally accepted that the lactic acid bacteria (LAB), a group of bacteria that ferment lactose to lactate, are a dominant population in bovine, goat, sheep and buffalo milk, prior to pasteurisation. The maternal gut is the principal source of commensal bacteria in the infant gut during the lactation stage, where breast milk acts as an intermediary for the transfer of G S & Mayo B (, Fernndez Finally, yeasts, and especially Candida species, can be opportunistic pathogens, causing infections in immunocompromised patients. I Voidarou The dominant, and subdominant, microorganisms present in raw milk can have a variety of influences on the flavour, taste and texture of raw milk-derived products (Fig.

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