Predicting fiber content in herbivore fecal samples using a multispecies NIRS model

Fiber is essential for rumen health, microbial fermentation, and the energy supply of herbivores. Even though the study of fecal fiber contents (neutral detergent fiber NDF, acid detergent fiber ADF, and acid detergent lignin ADL) using near-infrared reflectance spectroscopy (NIRS) has allowed investigating nutritional ecology of different herbivore species, NIRS calibrations are species-specific and require a large number of samples for predictions. A multispecies calibration would be an advantage since samples from different herbivores could be used to calibrate a model capable of predicting the fecal fiber content of other herbivores. To date, however, multispecies models have not been developed to predict fiber contents in the feces of herbivores. Here, we fill this gap by calibrating three fiber multispecies models (NDF, ADF and ADL) using fecal samples from domestic and wild herbivore species. We also evaluated the effect of incorporating sodium sulfite in fiber determination protocol. The initial dataset consisting of 445 samples of six herbivore species was used to calibrate (80% of the samples) and validate (20% of the samples) the models. Subsequently, 63 samples of five herbivores not included in the calibration set were used for the external validation of the model. Since sodium sulfite did not significantly improve fecal fiber prediction, our model was developed without this compound. The multispecies models obtained were highly accurate determining NDF, ADF and ADL (R2CAL, coefficient of determination in calibration, ≥ 0.93, R2VAL, coefficient of determination in validation, ≥ 0.91) and independent of external confounders. For external validation, the accuracy in predicting fecal samples in other herbivore species was also satisfactory, with consistently better values for NDF (R2VAL, 0.86-0.94) and ADF (R2VAL, 0.80-0.95) than for ADL (R2VAL, 0.66-0.89). We show that multispecies NIRS calibrations can be used with high accuracy to assess fecal fiber contents across diverse herbivore species. This finding represents a significant advance in the study of the nutritional ecology of herbivores with contrasting foraging patterns. In the future, widening the data range (e.g., species and locations) of the initial dataset could further improve the accuracy of these models.

Rapid Classification of Milk Using a Cost-Effective Near Infrared Spectroscopy Device and Variable Cluster-Support Vector Machine (VC-SVM) Hybrid Models

Removing fat from whole milk and adding water to milk to increase its volume are among the most common food fraud practices that alter the characteristics of milk. Usually, deviations from the expected fat content can indicate adulteration. Infrared spectroscopy is a commonly used technique for distinguishing pure milk from adulterated milk, even when it comes from different animal species. More recently, portable spectrometers have enabled in situ analysis with analytical performance comparable to that of benchtop instruments. Partial Least Square (PLS) analysis is the most popular tool for developing calibration models, although the increasing availability of portable near infrared spectroscopy (NIRS) has led to the use of alternative supervised techniques, including support vector machine (SVM). The aim of this study was to develop and implement a method based on the combination of a compact and low-cost Fourier Transform near infrared (FT-NIR) spectrometer and variable cluster-support vector machine (VC-SVM) hybrid model for the rapid classification of milk in accordance with EU Regulation EC No. 1308/2013 without any pre-treatment. The results obtained from the external validation of the VC-SVM hybrid model showed a perfect classification capacity (100% sensitivity, 100% specificity, MCC = 1) for the radial basis function (RBF) kernel when used to classify whole vs. not-whole and skimmed vs. not-skimmed milk samples. A strong classification capacity (94.4% sensitivity, 100% specificity, MCC = 0.95) was also achieved in discriminating semi-skimmed vs. not-semi-skimmed milk samples. This approach provides the dairy industry with a practical, simple and efficient solution to quickly identify skimmed, semi-skimmed and whole milk and detect potential fraud.

SVR Chemometrics to Quantify β-Lactoglobulin and α-Lactalbumin in Milk Using MIR

Protein content variation in milk can impact the quality and consistency of dairy products, necessitating access to in-line real time monitoring. Here, we present a chemometric approach for the qualitative and quantitative monitoring of β-lactoglobulin and α-lactalbumin, using mid-infrared spectroscopy (MIR). In this study, we employed Hotelling T2 and Q-residual for outlier detection, automated preprocessing using nippy, conducted wavenumber selection with genetic algorithms, and evaluated four chemometric models, including partial least squares, support vector regression (SVR), ridge, and logistic regression to accurately predict the concentrations of β-lactoglobulin and α-lactalbumin in milk. For the quantitative analysis of these two whey proteins, SVR performed the best to interpret protein concentration from 197 MIR spectra originating from 42 Cornell University samples of preserved pasteurized modified milk. The R2 values obtained for β-lactoglobulin and α-lactalbumin using leave one out cross-validation (LOOCV) are 92.8% and 92.7%, respectively, which is the highest correlation reported to date. Our approach introduced a combination of preprocessing automation, genetic algorithm-based wavenumber selection, and used Optuna to optimize the framework for tuning hyperparameters of the chemometric models, resulting in the best chemometric analysis of MIR data to quantitate β-lactoglobulin and α-lactalbumin to date.

Minerals and essential amino acids of bovine colostrum: Phenotypic variability and predictive ability of mid- and near-infrared spectroscopy

Colostrum quality and volume are fundamental for calves because it is the primary supplier of antibodies and the first source of energy, carbohydrates, lipids, proteins, minerals, and vitamins for the newborn. Assessing the detailed composition (i.e., AA and mineral content) of bovine colostrum (BC) on-line and at a reasonable cost would help dairy stakeholders such as farmers or veterinarians for precision feeding purposes and industries producing preparations containing BC such as foodstuff, supplements, and medicaments. In the present study we evaluated mid- (MIRS) and near-infrared spectroscopy (NIRS) prediction ability for AA and mineral composition of individual BC. Second, we the investigated the major factors affecting the phenotypic variability of such traits also evaluating the correlations with the Ig concentration. Results demonstrated that MIRS and NIRS were able to provide sufficiently accurate predictions for all the AA. The coefficient of determination in external validation (R2V) fell, in fact, within the range of 0.70 to 0.86, with the exception of Ile, His, and Met. Only some minerals reached a sufficient accuracy (i.e., Ca, P, S, and Mg; R2V ≥ 0.66) using MIRS, and also S (R2V = 0.87) using NIRS. Phenotypically, both parity and calving season affected the variability of these BC composition traits. Heifers' colostrum was the one with the greatest concentration of Ca and P, the 2 most abundant minerals. These minerals were however very low in cows calving in summer compared with the rest of the year. The pattern of AA across parities and calving season was not linear, likely because their variability was scarcely (or not) affected by these effects. Finally, samples characterized by high IgG concentration were those presenting on average greater concentration of AA. Findings suggest that infrared spectroscopy has the potential to be used to predict certain AA and minerals, outlining the possibility of implementing on-site analyses for the evaluation of the broad-sense BC quality.

Improved methods for mare milk analysis: Extraction and quantification of mare milk carbohydrates and assessment of FTIR-based macronutrient quantification

Accurately determining the macronutrient profile of mare milk is a precursor to studying how milk composition affects foals' growth and development. This study optimized and validated an extraction and quantification method for mare milk oligosaccharides, which make up a portion of the carbohydrate fraction of mare milk. Mare milk was extracted with chloroform and methanol, and oligosaccharides were selectively isolated from the carbohydrate fraction using porous-graphitized carbon solid-phase-extraction (SPE). Good recovery rates for milk oligosaccharides (between 70 and 100%) were achieved with the optimized method. This study also compared the use of Fourier-Transform infrared (FTIR) spectroscopy versus wet chemistry quantification methods for protein, fat, and lactose. The FTIR method produced statistically equivalent protein contents to the wet chemistry method, along with substantial savings in both analyst time and consumable consumption. FTIR analysis slightly underestimated the fat content of mare milk relative to the official wet chemistry method, with the difference between the methods increasing at higher fat contents. FTIR also overestimated the lactose content of mare milk and appeared to generate "lactose" values that included the milk oligosaccharides and thus represented the total carbohydrate (lactose and milk oligosaccharides) content of mare milk.

Cheese quality assessment by use of near-infrared spectroscopy

Dairy products are worldwide spread and have great commercial importance. Rapid and reliable analysis of cheese would be highly desirable both for the manufacturers and consumers. The results of experiments, related to the application of near-infrared spectroscopy for cheese quality estimation will be presented. Several kinds of Bulgarian white brine cheese - natural from cow milk, imitation products with vegetable oil, and cheese with different water content were investigated. Fatty acids composition of samples was determined by using gas chromatography and moisture content by the oven-dry method. Spectra of all tested samples were obtained with a scanning NIRQuest 512 (Ocean Optics, Inc.) instrument in the range of 900-1700 nm using a reflection fiber-optics probe. PLS models were developed for quantitative determination and SIMCA for classification. The misclassification rate of the SIMCA model for discrimination of natural cheese and imitation products with vegetable oil was 2.9%. Quantitative determination of water content based on NIR spectra showed high accuracy, Models for classification of cheese samples into 3 groups according to water content achieved 5.64% misclassification rate for the independent test set. Results showed the potential of near-infrared spectroscopy as a non-destructive and rapid screening tool for assessing cheese quality and detecting adulteration.

Authenticity and Typicity of Traditional Cheeses: A Review on Geographical Origin Authentication Methods

Food fraud, corresponding to any intentional action to deceive purchasers and gain an undue economical advantage, is estimated to result in a 10 to 65 billion US dollars/year economical cost worldwide. Dairy products, such as cheese, in particular cheeses with protected land- and tradition-related labels, have been listed as among the most impacted as consumers are ready to pay a premium price for traditional and typical products. In this context, efficient food authentication methods are needed to counteract current and emerging frauds. This review reports the available authentication methods, either chemical, physical, or DNA-based methods, currently used for origin authentication, highlighting their principle, reported application to cheese geographical origin authentication, performance, and respective advantages and limits. Isotope and elemental fingerprinting showed consistent accuracy in origin authentication. Other chemical and physical methods, such as near-infrared spectroscopy and nuclear magnetic resonance, require more studies and larger sampling to assess their discriminative power. Emerging DNA-based methods, such as metabarcoding, showed good potential for origin authentication. However, metagenomics, providing a more in-depth view of the cheese microbiota (up to the strain level), but also the combination of methods relying on different targets, can be of interest for this field.

Comparative evaluation of miniaturized and conventional NIR spectrophotometer for estimation of fatty acids in cheeses

The miniaturization of near-infrared spectrometers has been growing rapidly. Several designs are now available, but there is a lack of understanding of how spectral data from these designs are affected by complex matrices and what are the limitations when compared to established systems. This study compares a popular miniaturized NIR device based on Hadamard-transform spectrometer (named miniaturized NIR) with a system based on dispersive spectrometer (named handheld-NIR) to assess: 1) their predictive performance; 2) the effect of a complex matrix on the performance, and 3) ability to discriminate multiples compounds in that matrix. The devices were challenged with a wide range of cheese types (n = 36) from different species (cow, goat, ewe and buffalo), brands (n = 30), countries of origin (n = 9) and with a broad range of cheese matrices (soft, fresh, semi-hard, hard and aged) to predict fat composition. Spectra were collected non-invasively with no sample preparation. Three wavelength ranges from handheld NIR were compared to miniaturized NIR based on two modelling approaches were used: a linear (Partial Least Square - PLS) and a non-linear (Support Vector Machine - SVM). The important wavelengths for each model were identified and used to assess the ability of the spectral data to differentiate among fatty acids. The highest prediction performance was observed for saturated fatty acids (C4.0, C14.0, C15.0 C16.0, total SCF and total SFA) with the RPD_EXT-VAL for the external validation dataset presenting values higher than 3 and the coefficient of determination for the external validation dataset (R²_EXT-VAL) higher than 0.89, mostly for SVM models. The sum of fatty acids also shows good prediction performance with RPD_EXT-VAL higher than 3 and R²_EXT-VAL higher than 0.89. Models with RPD_EXT-VAL between 2 and 3 includes: C6.0; C17.0; C18.0; C10.1; C16.1; C17.1; iso.C15.0; iso.C.16; iso.C17; C18.1.c11; C18.1.c9; anteiso C17; total MUFA; and total BCFA. The cheese matrix affected the linearity between spectral data and fatty acids concentration requiring a more complex model (SVM), but this effect was not enhanced by the instrument type. It was shown that the spectral information allows discrimination among fatty acids and this ability was not affected by the type of instrument. These findings demonstrated that the miniaturized NIR can be directly applied to a cheese matrix to monitor fatty acid composition with results equivalent to an optical-based design.

Amino Acid Fingerprinting of Authentic Nonfat Dry Milk and Skim Milk Powder and Effects of Spiking with Selected Potential Adulterants

A collaborative study was undertaken in which five international laboratories participated to determine amino acid fingerprints in 39 authentic nonfat dry milk (NFDM)/skim milk powder (SMP) samples. A rapid method of amino acid analysis involving microwave-assisted hydrolysis followed by ultra-high performance liquid chromatography-ultraviolet detection (UHPLC-UV) was used for quantitation of amino acids and to calculate their distribution. The performance of this rapid method of analysis was evaluated and was used to determine the amino acid fingerprint of authentic milk powders. The distribution of different amino acids and their predictable upper and lower tolerance limits in authentic NFDM/SMP samples were established as a reference. Amino acid fingerprints of NFDM/SMP were compared with selected proteins and nitrogen rich compounds (proteins from pea, soy, rice, wheat, whey, and fish gelatin) which can be potential economically motivated adulterants (EMA). The amino acid fingerprints of NFDM/SMP were found to be affected by spiking with pea, soy, rice, whey, fish gelatin and arginine among the investigated adulterants but not by wheat protein and melamine. The study results establish an amino acid fingerprint of authentic NFDM/SMP and demonstrate the utility of this method as a tool in verifying the authenticity of milk powders and detecting their adulteration.

New insights into the raw milk microbiota diversity from animals with a different genetic predisposition for feed efficiency and resilience to mastitis

The main objective of this study was to assess the microbiota diversity in milk samples collected from Holstein cows with different estimated breeding values for predicted feed efficiency, milk coagulation, resilience to mastitis, and consequently, to study its effects on milk quality. One hundred and twenty milk samples were collected in two seasons (summer and winter) from different commercial dairy farms in the Nord-east of Italy. For each trait, 20 animals divided into two groups of the high (10 cows) and the low (10 cows) were selected to study the microbiota profile using 16S rRNA metabarcoding sequencing. The alpha and beta diversity analysis revealed significant differences between the high and the low groups for feed efficiency and resilience to mastitis, while no significant difference was detected for milk coagulation. Moreover, remarkable differences among the taxa were detected between the two seasons, where the winter was more diverse than summer when applied the Chao1 index. Lastly, the linear discriminant analysis (LDA) effect size (LEfSe) indicated Aerococcus, Corynebacterium, Facklamia, and Psychrobacter taxa with more abundance in the high group of feed efficiency, whereas, in resilience to mastitis, only two genera of Mycoplana and Rhodococcus were more abundant in the low group. In addition, LEfSe analysis between the seasons showed significant differences in the abundance of Bacteroides, Lactobacillus, Corynebacterium, Escherichia, Citrobacter, Pantoea, Pseudomonas, and Stenotrophomonas. These findings indicate that the different genetic predisposition for feed efficiency and resilience to mastitis could affect the raw milk microbiota and, consequently, its quality. Moreover, we found more abundance of mastitis-associated bacteria in the milk of dairy cows with a higher feed efficiency index.

Near-infrared techniques for fraud detection in dairy products: A review

The dairy products sector is an important part of the food industry, and their consumption is expected to grow in the next 10 years. Therefore, the authentication of these products in a faster and precise way is required for the sake of public health. This review proposes the use of near-infrared techniques for the detection of food fraud in dairy products as they are faster, nondestructive, environmentally friendly, do not require sample preparation, and allow multiconstituent analysis. First, we have described frequent forms of food fraud in dairy products and the application of traditional techniques for their detection, highlighting gaps and counterproductive characteristics for the actual global food chain, as longer sample preparation time and use of reagents. Then, the application of near-infrared spectroscopy and hyperspectral imaging for the detection of food fraud mainly in cheese, butter, and yogurt are described. As these techniques depend on model development, the coverage of different dairy products by the literature will promote the identification of food fraud in a faster and reliable way.

Effectiveness of visible - Near infrared spectroscopy coupled with simulated annealing partial least squares analysis to predict immunoglobulins G, A, and M concentration in bovine colostrum

Visible - near infrared spectroscopy coupled with variable selection using simulated annealing PLS regression was tested to predict immunoglobulin fractions (g/L) of bovine colostrum, namely IgG, IgA and IgM. Immunoglobulins were quantified in 678 samples using the gold standard radial immunodiffusion. Samples were divided in calibration (50%) and validation (50%) datasets. Maximum number of selected variables were limited to 200 and root mean squared error in cross validation (RMSE_CV) was used as loss function. Performance of the final model developed using the calibration dataset was assessed on the validation dataset. Overall, simulated annealing PLS improved validation RMSE_CV compared to ordinary PLS regression by 3% to 17%. The present study demonstrated the effectiveness of the calibration model for accurate quantification of IgG, the most abundant immunoglobulin of bovine colostrum (RMSE_CV = 13.28 g/L; R² = 0.83). These outcomes could be useful to assess colostrum quality intended for animal and human usage.

Invited review: A comprehensive review of visible and near-infrared spectroscopy for predicting the chemical composition of cheese

Substantial research has been carried out on rapid, nondestructive, and inexpensive techniques for predicting cheese composition using spectroscopy in the visible and near-infrared radiation range. Moreover, in recent years, new portable and handheld spectrometers have been used to predict chemical composition from spectra captured directly on the cheese surface in dairies, storage facilities, and food plants, removing the need to collect, transport, and process cheese samples. For this review, we selected 71 papers (mainly dealing with prediction of the chemical composition of cheese) and summarized their results, focusing our attention on the major sources of variation in prediction accuracy related to cheese variability, spectrometer and spectra characteristics, and chemometrics techniques. The average coefficient of determination obtained from the validation samples ranged from 86 to 90% for predicting the moisture, fat, and protein contents of cheese, but was lower for predicting NaCl content and cheese pH (79 and 56%, respectively). There was wide variability with respect to all traits in the results of the various studies (standard deviation: 9-30%). This review draws attention to the need for more robust equations for predicting cheese composition in different situations; the calibration data set should consist of representative cheese samples to avoid bias due to an overly specific field of application and ensure the results are not biased for a particular category of cheese. Different spectrometers have different accuracies, which do not seem to depend on the spectrum extension. Furthermore, specific areas of the spectrum-the visible, infrared-A, or infrared-B range-may yield similar results to broad-range spectra; this is because several signals related to cheese composition are distributed along the spectrum. Small, portable instruments have been shown to be viable alternatives to large bench-top instruments. Last, chemometrics (spectra pre-treatment and prediction models) play an important role, especially with regard to difficult-to-predict traits. A proper, fully independent, validation strategy is essential to avoid overoptimistic results.

The concentrations of immunoglobulins in bovine colostrum determined by the gold standard method are genetically correlated with their near-infrared prediction

Background

The quality of colostrum administered to calves is based on its concentration in immunoglobulins G (IgG, g/L). Immunoglobulins A (IgA) and M (IgM) are also present but at a lower level. The gold standard reference analysis for these traits, radial immunodiffusion, is time-consuming and expensive. In order to define breeding strategies that are aimed at improving colostrum quality in dairy cattle, a large amount of data is needed, and the use of indicator traits would be beneficial. In the study presented here, we explored the heritabilities of reference (radial immunodiffusion) and near infrared-predicted IgG, IgA, and IgM concentrations and estimated their genetic correlations. First, the colostrum of 765 Holstein cows from nine herds was sampled to perform a reference analysis and the near-infrared spectra (400–2500 nm) were stored. We used a calibration set (28% of the initial samples) that was representative of the herds and cow parity orders to develop prediction equations for IgG, IgA, and IgM concentrations. Finally, these traits were predicted in the validation set (72% of the initial samples) to estimate genetic parameters for the predictions. Genetic correlations between reference and predicted values of each trait were estimated through bivariate linear animal models.

Results

The three near-infrared-predicted immunoglobulin fractions were genetically correlated with their reference value. In particular, the reference and predicted IgG concentrations were strongly correlated at both the genetic (0.854 ± 0.314) and phenotypic level (0.767 ± 0.019). Weaker associations were observed for IgA and IgM concentrations, which were predicted with lower accuracy compared to IgG. Simulation analyses suggested that improving colostrum quality by selective breeding in Holstein cattle based on near-infrared predicted colostrum immunoglobulins concentrations is feasible. In addition, less than 10 mL of colostrum are needed for spectra acquisition and thus implementation of such analyses is possible in the near future.

Conclusions

The concentrations of colostrum immunoglobulins can be predicted from near-infrared spectra and the genetic correlation between the reference and the predicted traits is positive and favourable, in spite of the large standard errors of the estimates. Near-infrared spectroscopy can be exploited in selective breeding of dairy cattle to improve colostral immunoglobulins concentration.

Role of Pascalization in Milk Processing and Preservation: A Potential Alternative towards Sustainable Food Processing

Renewed technology has created a demand for foods which are natural in taste, minimally processed, and safe for consumption. Although thermal processing, such as pasteurization and sterilization, effectively limits pathogenic bacteria, it alters the aroma, flavor, and structural properties of milk and milk products. Nonthermal technologies have been used as an alternative to traditional thermal processing technology and have the ability to provide safe and healthy dairy products without affecting their nutritional composition and organoleptic properties. Other than nonthermal technologies, infrared spectroscopy is a nondestructive technique and may also be used for predicting the shelf life and microbial loads in milk. This review explains the role of pascalization or nonthermal techniques such as high-pressure processing (HPP), pulsed electric field (PEF), ultrasound (US), ultraviolet (UV), cold plasma treatment, membrane filtration, micro fluidization, and infrared spectroscopy in milk processing and preservation.

Recent Advances in Portable and Handheld NIR Spectrometers and Applications in Milk, Cheese and Dairy Powders

Quality and safety monitoring in the dairy industry is required to ensure products meet a high-standard based on legislation and customer requirements. The need for non-destructive, low-cost and user-friendly process analytical technologies, targeted at operators (as the end-users) for routine product inspections is increasing. In recent years, the development and advances in sensing technologies have led to miniaturisation of near infrared (NIR) spectrometers to a new era. The new generation of miniaturised NIR analysers are designed as compact, small and lightweight devices with a low cost, providing a strong capability for on-site or on-farm product measurements. Applying portable and handheld NIR spectrometers in the dairy sector is increasing; however, little information is currently available on these applications and instrument performance. As a result, this review focuses on recent developments of handheld and portable NIR devices and its latest applications in the field of dairy, including chemical composition, on-site quality detection, and safety assurance (i.e., adulteration) in milk, cheese and dairy powders. Comparison of model performance between handheld and bench-top NIR spectrometers is also given. Lastly, challenges of current handheld/portable devices and future trends on implementing these devices in the dairy sector is discussed.

A combined metabolomics and peptidomics approach to discriminate anomalous rind inclusion levels in Parmigiano Reggiano PDO grated hard cheese from different ripening stages

Parmigiano Reggiano is a hard cheese with a Protected Designation of Origin (PDO) certification that also applies to the grated product. The percentage of rind in grated Parmigiano Reggiano is regulated by the PDO production Specification and must not exceed the limit of 18% (w/w). The present study evaluates the potential of an untargeted foodomics approach to detect anomalous inclusions of rind in grated Parmigiano Reggiano cheese. In particular, a combined metabolomics and peptidomics approach was used to detect potential markers of counterfeits (rind > 18%). In the framework of realistic food integrity purposes, non-Parmigiano Reggiano grated samples and different ripening times were also considered. Untargeted metabolomics allowed detecting 347 compounds, with a prevalence of amino acids and peptide derivatives, followed by fatty acyls and other compounds (such as lactones, ketones, and aldehydes) typically related to proteolysis and lipolysis events. Overall, the unsupervised multivariate statistics showed that the ripening time plays a hierarchically higher impact than rind inclusion in determining the main differences in the chemical profiles detected. Interestingly, supervised statistics highlighted distinctive markers for ripening time and rind inclusion, with only 16 common discriminant compounds being shared between the two conditions. The best markers of rind inclusion > 18% were 2-hydroxyadenine (VIP score = 1.937; AUC value = 0.83) and the amino acid derivatives argininic acid (VIP score = 1.462; AUC value = 0.75) and 5-hydroxyindole acetaldehyde (VIP score = 1.710; AUC value = 0.86). Interestingly, the medium-chain aldehyde 4-hydroperoxy-2-nonenal was a common marker of both ripening time and anomalous rind inclusion (>18%), likely arising from the lipid oxidation processes. Finally, among potential marker peptides of rind inclusion, the alpha-S1 casein proteolytic product (F)FVAPFPEVFGK(E) could be identified.

FT-MIR Analysis of Water-Soluble Extracts during the Ripening of Sheep Milk Cheese with Different Phospholipid Content

The purpose of this work was to study the suitability of the water-soluble extracts (WSE) of semi-hard sheep milk cheese for analysis by diffuse reflectance Fourier transform mid-infrared spectroscopy (FT-MIR) and the development of classification models using discriminant analysis and based on cheese age or phospholipid content. WSE was extracted from three types of sheep milk cheeses (full-fat, reduced-fat and reduced-fat fortified with lyophilized sweet sheep buttermilk) at various stages of ripening from six to 168 days and lyophilized. The first model used 1854–1381 and 1192–760 cm−1 regions of the first-derivative spectra and successfully differentiated samples of different age, based on changes in the water-soluble products of ripening biochemical events. The second model used the phospholipid absorbance spectral regions (3012–2851, 1854–1611 and 1192–909 cm−1) to successfully discriminate cheeses of markedly different phospholipid content. Cheese WSE was found suitable for FT-MIR analysis. According to the results, a fast and simple method to monitor cheese ripening based on water-soluble substances has been developed. Additionally, the results indicated that a considerable amount of phospholipids migrates to the cheese WSE and that FT-MIR can be a useful tool for their assessment.

Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

BACKGROUND

Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. While there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Using imputed whole-genome sequence for 38,085 mixed-breed New Zealand dairy cattle, we conducted GWAS on 895 individual FT-MIR wavenumber phenotypes, and assessed the value of these direct phenotypes for identifying candidate causal genes and variants, and improving our understanding of the physico-chemical properties of milk.

RESULTS

Separate GWAS conducted for each of 895 individual FT-MIR wavenumber phenotypes, identified 450 1-Mbp genomic regions with significant FT-MIR wavenumber QTL, compared to 246 1-Mbp genomic regions with QTL identified for FT-MIR predicted milk composition traits. Use of mammary RNA-seq data and gene annotation information identified 38 co-localized and co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in the ABO gene that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, we examined the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum. This revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk.

CONCLUSIONS

This study demonstrates the utility of FT-MIR wavenumber phenotypes for improving our understanding of milk composition, presenting a larger number of QTL and putative causative genes and variants than found from FT-MIR predicted composition traits. Examining patterns of significance across the mid-infrared spectrum for loci of interest further highlighted commonalities of association, which likely reflects the physico-chemical properties of milk constituents.

The Combination of Vibrational Spectroscopy and Chemometrics for Analysis of Milk Products Adulteration

Milk products obtained from cow, goat, buffalo, sheep, and camel as well as fermented forms such as cheese, yogurt, kefir, and butter are in a category of the most nutritious foods due to their high contents of high protein contributing to total daily energy intake. For certain reasons, high price milk products may be adulterated with low-quality ones or with foreign substances such as melamine and formalin which are added into them; therefore, a comprehensive review on analytical methods capable of detecting milk adulteration is needed. The objective of this narrative review is to highlight the use of vibrational spectroscopies (near infrared, mid infrared, and Raman) combined with multivariate analysis for authentication of milk products. Articles, conference reports, and abstracts from several databases including Scopus, PubMed, Web of Science, and Google Scholar were used in this review. By selecting the correct conditions (spectral treatment, normal versus derivative spectra at wavenumbers region, and chemometrics techniques), vibrational spectroscopy is a rapid and powerful analytical technique for detection of milk adulteration. This review can give comprehensive information for selecting vibrational spectroscopic methods combined with chemometrics techniques for screening the adulteration practice of milk products.

Use of Fourier Transform Infrared Spectroscopy for Monitoring the Shelf Life and Safety of Yogurts Supplemented With a Lactobacillus plantarum Strain With Probiotic Potential

The current study aimed to explore the performance of a probiotic Lactobacillus strain as an adjunct culture in yogurt production and to assess Fourier transform infrared spectroscopy as a rapid, noninvasive analytical technique to evaluate the quality and the shelf life of yogurt during storage. In this respect, bovine milk (full-fat) was inoculated with the typical yogurt starter culture without (control case) or with the further addition of Lactobacillus plantarum T571 as an adjunct (probiotic case). The milk was also inoculated with a cocktail mixture of three strains of Listeria monocytogenes in two different initial levels of inoculum, and the fermentation process was followed. Accordingly, yogurt samples were stored at 4 and 12°C, and microbiological, physicochemical, molecular, and sensory analyses were performed during storage. Results showed that the lactic acid bacteria exceeded 7 log CFU/g during storage in all samples, where the probiotic samples displayed higher acidity, lower pH, and reduced counts of Lb. monocytogenes in a shorter period than the control ones at both temperatures. Pulsed-field gel electrophoresis verified the presence of the probiotic strain until the end of storage at both temperatures and in adequate amounts, whereas the survival and the distribution of Listeria strains depended on the case. The sensory evaluation showed that the probiotic samples had desirable organoleptic characteristics, similar to the control. Finally, the spectral data collected from the yogurt samples during storage were correlated with microbiological counts and sensory data. Partial least squares and support vector machine regression and classification models were developed to provide quantitative estimations of yogurt microbiological counts and qualitative estimations of their sensory status, respectively, based on Fourier transform infrared fingerprints. The developed models exhibited satisfactory performance, and the acquired results were promising for the rapid estimation of the microbiological counts and sensory status of yogurt.

Variation of immunoglobulins G, A, and M and bovine serum albumin concentration in Holstein cow colostrum

Immunoglobulins G (IgG), A (IgA), and M (IgM) represent 70-80% of total proteins in cattle colostrum and are essential for the passive transfer of antibodies from the dam to the calf. Considering the practical difficulties of colostrum sample collection and the high cost of analysis, non-genetic sources of variation of the three immunoglobulins fractions have been scarcely studied together on a large scale in dairy cows. In the present study, IgG, IgA, IgM, and bovine serum albumin (BSA) were determined in colostrum samples of Holstein cows through bovine-specific radial immunodiffusion kits; such phenotypes allowed to investigate the effects of parity, herd, and calving season, and interactions. Only the first colostrum was considered in the present study, as the calf was separated from the dam immediately after birth and was not allowed to suckle. The average of IgG (n = 676), IgA (n = 573), IgM (n = 658), total immunoglobulins (n = 525), and BSA (n = 614) was 91.31, 4.20, 105.99, 5.05, and 2.47 g/L, respectively, and all traits positively correlated to each other. Overall, the immunoglobulins were less concentrated in colostrum of first- and second-parity cows than later-parity cows. These findings suggest that colostrum quality, based on Ig, is overall greater in cows that experienced more than two lactations, likely due to a greater experience of the immune system and to a wider immune heritage compared to younger cows. As regards the effect of calving season, the concentration of all Ig tended to be generally greater in colostrum sampled from August to November. Moreover, there were differences in IgG, IgA, and IgM concentration among the nine herds involved. Future studies will investigate the relationships of these traits with yield, and gross and detailed composition of bovine colostrum and will consider their genetic background to evaluate potential selection strategies to improve colostrum quality.

Genetic analysis on infrared-predicted milk minerals for Danish dairy cattle

A group of milk components that has shown potential to be predicted with milk spectra is milk minerals. Milk minerals are important for human health and cow health. Having an inexpensive and fast way to measure milk mineral concentrations would open doors for research, herd management, and selective breeding. The first aim of this study was to predict milk minerals with infrared milk spectra. Additionally, milk minerals were predicted with infrared-predicted fat, protein, and lactose content. The second aim was to perform a genetic analysis on infrared-predicted milk minerals, to identify QTL, and estimate variance components. For training and validating a multibreed prediction model for individual milk minerals, 264 Danish Jersey cows and 254 Danish Holstein cows were used. Partial least square regression prediction models were built for Ca, Cu, Fe, K, Mg, Mn, Na, P, Se, and Zn based on 80% of the cows, selected randomly. Prediction models were externally validated with 8 herds based on the remaining 20% of the cows. The prediction models were applied on a population of approximately 1,400 Danish Holstein cows with 5,600 infrared spectral records and 1,700 Danish Jersey cows with 7,200 infrared spectral records. Cows from this population had 50k imputed genotypes. Prediction accuracy was good for P and Ca, with external R² ≥ 0.80 and a relative prediction error of 5.4% for P and 6.3% for Ca. Prediction was moderately good for Na with an external R² of 0.63, and a relative error of 18.8%. Prediction accuracies of milk minerals based on infrared-predicted fat, protein, and lactose content were considerably lower than those based on the infrared milk spectra. This shows that the milk infrared spectrum contains valuable information on milk minerals, which is currently not used. Heritability for infrared-predicted Ca, Na, and P varied from low (0.13) to moderate (0.36). Several QTL for infrared-predicted milk minerals were observed that have been associated with gold standard milk minerals previously. In conclusion, this study has shown infrared milk spectra were good at predicting Ca, Na, and P in milk. Infrared-predicted Ca, Na, and P had low to moderate heritability estimates.

Comprehensive Review on Application of FTIR Spectroscopy Coupled with Chemometrics for Authentication Analysis of Fats and Oils in the Food Products

Currently, the authentication analysis of edible fats and oils is an emerging issue not only by producers but also by food industries, regulators, and consumers. The adulteration of high quality and expensive edible fats and oils as well as food products containing fats and oils with lower ones are typically motivated by economic reasons. Some analytical methods have been used for authentication analysis of food products, but some of them are complex in sampling preparation and involving sophisticated instruments. Therefore, simple and reliable methods are proposed and developed for these authentication purposes. This review highlighted the comprehensive reports on the application of infrared spectroscopy combined with chemometrics for authentication of fats and oils. New findings of this review included (1) FTIR spectroscopy combined with chemometrics, which has been used to authenticate fats and oils; (2) due to as fingerprint analytical tools, FTIR spectra have emerged as the most reported analytical techniques applied for authentication analysis of fats and oils; (3) the use of chemometrics as analytical data treatment is a must to extract the information from FTIR spectra to be understandable data. Next, the combination of FTIR spectroscopy with chemometrics must be proposed, developed, and standardized for authentication and assuring the quality of fats and oils.

Milk as a Complex Multiphase Polydisperse System: Approaches for the Quantitative and Qualitative Analysis

Milk is a product that requires quality control at all stages of production: from the dairy farm, processing at the dairy plant to finished products. Milk is a complex multiphase polydisperse system, whose components not only determine the quality and price of raw milk, but also reflect the physiological state of the herd. Today’s production volumes and rates require simple, fast, cost-effective, and accurate analytical methods, and most manufacturers want to move away from methods that use reagents that increase analysis time and move to rapid analysis methods. The review presents methods for the rapid determination of the main components of milk, examines their advantages and disadvantages. Optical spectroscopy is a fast, non-destructive, precise, and reliable tool for determination of the main constituents and common adulterants in milk. While mid-infrared spectroscopy is a well-established off-line laboratory technique for the routine quality control of milk, near-infrared technologies provide relatively low-cost and robust solutions suitable for on-site and in-line applications on milking farms and dairy production facilities. Other techniques, discussed in this review, including Raman spectroscopy, atomic spectroscopy, molecular fluorescence spectroscopy, are also used for milk analysis but much less extensively. Acoustic methods are also suitable for non-destructive on-line analysis of milk. Acoustic characterization can provide information on fat content, particle size distribution of fat and proteins, changes in the biophysical properties of milk over time, the content of specific proteins and pollutants. The basic principles of ultrasonic techniques, including transmission, pulse-echo, interferometer, and microbalance approaches, are briefly described and milk parameters measured with their help, including frequency ranges and measurement accuracy, are given.

Application of a Handheld Near-Infrared Spectrometer to Predict Gelatinized Starch, Fiber Fractions, and Mineral Content of Ground and Intact Extruded Dry Dog Food

Simple Summary

The pet food industry is interested in performing fast analyses to control the nutritional quality of their products. Despite having some limitations related to the need to modify the production process or to have a laboratory to prepare the samples for analysis through desktop instruments, near-infrared spectroscopy is one of the most used technologies for inexpensive analysis of foodstuffs. Thus, the miniaturization of infrared devices allows a wider industrial applicability of this technique. Information on the use of miniaturized infrared tools in the pet food sector is currently very limited, and the present research is the first attempt to predict the total and gelatinized starch, insoluble fibrous fractions, and mineral content of ground and intact dry pet food using the handheld NIR scanner SCiO™. Results from the current study revealed no significant differences in the predictive ability of the instrument using both ground and intact samples. The instrument offers a potential for screening purposes of both total and gelatinized starch, revealing the potential to monitor their content and ratio in commercial dog food on a large scale. Improvements such as widening the wavelength range is expected to increase prediction models’ accuracy.

Abstract

The aim of the present study was to investigate the ability of a handheld near-infrared spectrometer to predict total and gelatinized starch, insoluble fibrous fractions, and mineral content in extruded dry dog food. Intact and ground samples were compared to determine if the homogenization could improve the prediction performance of the instrument. Reference analyses were performed on 81 samples for starch and 99 for neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and minerals, and reflectance infrared spectra (740 to 1070 nm) were recorded with a SCiO™ near-infrared (NIR) spectrometer. Prediction models were developed using modified partial least squares regression and both internal (leave-one-out cross-validation) and external validation. The best prediction models in cross-validation using ground samples were obtained for gelatinized starch (residual predictive deviation, RPD = 2.54) and total starch (RPD = 2.33), and S (RPD = 1.92), while the best using intact samples were obtained for gelatinized starch (RPD = 2.45), total starch (RPD = 2.08), and K (RPD = 1.98). Through external validation, the best statistics were obtained for gelatinized starch, with an RPD of 2.55 and 2.03 in ground and intact samples, respectively. Overall, there was no difference in prediction models accuracy using ground or intact samples. In conclusion, the miniaturized NIR instrument offers the potential for screening purposes only for total and gelatinized starch, S, and K, whereas the results do not support its applicability for the other traits.

Bayesian Discriminant Analysis of Yogurt Products Based on Raman Spectroscopy

Background

The quality discrimination of dairy products is an important basis on which to achieve quality assurance.

Objective

Taking the discriminant analysis of brand yogurt products as an example, a new rapid discriminant method can be constructed.

Method

The first three principal components were selected as the pattern vectors of the samples. Then, at random, 75% of the samples were collected as a training set, and their mean values and covariance matrices were calculated to construct a Gauss Bayesian discriminant model. The remaining 25% of samples were employed as a test set, and the pattern vectors of each sample were input into the above model. Next, the posterior probability of each sample in relation to each category could be obtained. Results: The category corresponding to the maximum posterior probability as the brand classification of each sample was defined.

Conclusions

We constructed a Gauss Bayesian discriminant model to discriminate these different yogurt products after the principal component feature extraction of Raman properties. The results indicate the rationality and wide application prospects of this approach.

Highlights

A fast dairy product discriminant method based on Gauss Bayesian model and Raman spectroscopy was established.

At-line Prediction of Gelatinized Starch and Fiber Fractions in Extruded Dry Dog Food Using Different Near-Infrared Spectroscopy Technologies

Simple Summary

Starch is a non-fibrous carbohydrate that represents an important percentage of pet food composition. The degree of its gelatinization, due to the cooking process, can be a useful indicator of starch digestibility in the diet. Moreover, fiber fractions are important for animals’ health and nutritional status, so pet food industry is interested in the development of an easy and cost-effective method to measure these parameters. Results of this study revealed the applicability of visible/near-infrared spectroscopy to predict total and gelatinized starch, neutral detergent fiber, acid detergent fiber, and acid detergent lignin in pet food. On the other hand, near-infrared transmittance technology showed a scarce accuracy. The developed prediction models for total and gelatinized starch and fiber fractions using visible/near-infrared spectroscopy could be applied during the manufacturing process to perform quality controls.

Abstract

This study aimed to assess the feasibility of visible/near-infrared reflectance (Vis-NIR) and near-infrared transmittance (NIT) spectroscopy to predict total and gelatinized starch and fiber fractions in extruded dry dog food. Reference laboratory analyses were performed on 81 samples, and the spectrum of each ground sample was obtained through Vis-NIR and NIT spectrometers. Prediction equations for each instrument were developed by modified partial least squares regressions and validated by cross- (CrV) and external validation (ExV) procedures. All studied traits were better predicted by Vis-NIR than NIT spectroscopy. With Vis-NIR, excellent prediction models were obtained for total starch (residual predictive deviation; RPD_CrV = 6.33; RPD_ExV = 4.43), gelatinized starch (RPD_CrV = 4.62; RPD_ExV = 4.36), neutral detergent fiber (NDF; RPD_CrV = 3.93; RPD_ExV = 4.31), and acid detergent fiber (ADF; RPD_CrV = 5.80; RPD_ExV = 5.67). With NIT, RPD_CrV ranged from 1.75 (ADF) to 2.61 (acid detergent lignin, ADL) and RPD_ExV from 1.71 (ADL) to 2.16 (total starch). In conclusion, results of the present study demonstrated the feasibility of at-line Vis-NIR spectroscopy in predicting total and gelatinized starch, NDF, and ADF, with lower accuracy for ADL, whereas results do not support the applicability of NIT spectroscopy to predict those traits.

Mid-infrared spectrometry prediction of the cheese-making properties of raw Montbéliarde milks from herds and cheese dairy vats used for the production of Protected Designation of Origin and Protected Geographical Indication cheeses in Franche-Comté

Franche-Comté is the primary producing region of Protected Designation of Origin cheeses in France. Normally, mid-infrared (MIR) prediction models for cheese-making property (CMP) traits are developed using individual bovine milks. However, considering the requests of all actors in the dairy sector, the present study aimed to assess the feasibility of MIR spectroscopy to develop CMP equations of Montbéliarde herd and dairy vat milks. For this purpose, 22 CMP traits were analyzed on samples collected in 2016 (half in February-March and half in May-June) from 100 commercial herds and 70 dairy vats (55 cheese dairies) located in Franche-Comté. These characteristics included 11 rennet coagulation traits and 8 lactic acidification traits measured in either soft cheese or pressed cooked cheese conditions and 3 laboratory curd yields. Models of MIR prediction for each of the 22 CMP traits were built using partial least squares regression with external validation by dividing the data set into calibration (70%) and validation (30%) sets. We confirmed that the variability of milk traits depends largely on the production scale and is higher for individual milk than for herd milk and even higher for vat milk. The best prediction models were obtained in herd milk samples for curd yields expressed in dry matter or fresh, with a coefficient of determination (R²) in external validation of 0.78 and 0.77, respectively. As with individual milk, these traits are closely related to the gross composition of the milk and therefore easier to predict by MIR spectroscopy. However, these curd yield traits were poorly predicted (R² = 0.58) in vat milk samples due to their lower variability. In herd milk samples, prediction models of other CMP traits were poorly accurate except for the ratio of the time to obtain a standard firmness to the rennet coagulation time in soft cheese or pressed cooked cheese conditions, which showed R² > 0.66 in external validation. Such trait is important in qualifying the behavior of milk during cheese production. Prediction models of other CMP traits for either herd or vat milk samples had poor accuracy, and further work is needed to improve their performance.

The evolving role of Fourier-transform mid-infrared spectroscopy in genetic improvement of dairy cattle

Over the last 100 years, significant advances have been made in the characterisation of milk composition for dairy cattle improvement programs. Technological progress has enabled a shift from labour intensive, on-farm collection and processing of samples that assess yield and fat levels in milk, to large-scale processing of samples through centralised laboratories, with the scope extended to include quantification of other traits. Fourier-transform mid-infrared (FT-MIR) spectroscopy has had a significant role in the transformation of milk composition phenotyping, with spectral-based predictions of major milk components already being widely used in milk payment and animal evaluation systems globally. Increasingly, there is interest in analysing the individual FT-MIR wavenumbers, and in utilising the FT-MIR data to predict other novel traits of importance to breeding programs. This includes traits related to the nutritional value of milk, the processability of milk into products such as cheese, and traits relevant to animal health and the environment. The ability to successfully incorporate these traits into breeding programs is dependent on the heritability of the FT-MIR predicted traits, and the genetic correlations between the FT-MIR predicted and actual trait values. Linking FT-MIR predicted traits to the underlying mutations responsible for their variation can be difficult because the phenotypic expression of these traits are a function of a diverse range of molecular and biological mechanisms that can obscure their genetic basis. The individual FT-MIR wavenumbers give insights into the chemical composition of milk and provide an additional layer of granularity that may assist with establishing causal links between the genome and observed phenotypes. Additionally, there are other molecular phenotypes such as those related to the metabolome, chromatin accessibility, and RNA editing that could improve our understanding of the underlying biological systems controlling traits of interest. Here we review topics of importance to phenotyping and genetic applications of FT-MIR spectra datasets, and discuss opportunities for consolidating FT-MIR datasets with other genomic and molecular data sources to improve future dairy cattle breeding programs.

Short communication: Investigation of the temporal relationships between milk mid-infrared predicted biomarkers and lameness events in later lactation

This study reports on the exploration of temporal relationships between milk mid-infrared predicted biomarkers and lameness events. Lameness in dairy cows is an issue that can vary greatly in severity and is of concern for both producers and consumers. Metabolic disorders are often associated with lameness. However, lameness can arise weeks or even months after the metabolic disorder, making the detection of causality difficult. We already use mid-infrared technology to predict major milk components, such as fat or protein, during routine milk recording and for milk payment. It was recently shown that this technology can also be used to predict novel biomarkers linked to metabolic disorders in cows, such as oleic acid (18:1 cis-9), β-hydroxybutyrate, acetone, and citrate in milk. We used these novel biomarkers as proxies for metabolic issues. Other studies have explored the possibility of using mid-infrared spectra to predict metabolic diseases and found it (potentially) usable for indicating classes of metabolic problems. We wanted to explore the possible relationship between mid-infrared-based metabolites and lameness over the course of lactation. In total, data were recorded from 6,292 cows on 161 farms in Austria. Lameness data were recorded between March 2014 and March 2015 and consisted of 37,555 records. Mid-infrared data were recorded between July and December 2014 and consisted of 9,152 records. Our approach consisted of fitting preadjustments to the data using fixed effects, computing pair-wise correlations, and finally applying polynomial smoothing of the correlations for a given biomarker at a certain month in lactation and the lameness events scored on severity scale from sound or non-lame (lameness score of 1) to severely lame (lameness score of 5) throughout the lactation. The final correlations between biomarkers and lameness scores were significant, but not high. However, for the results of the present study, we should not look at the correlations in terms of absolute values, but rather as indicators of a relationship through time. When doing so, we can see that metabolic problems occurring in mo 1 and 3 seem more linked to long-term effects on hoof and leg health than those in mo 2. However, the quantity (only 1 pair-wise correlation exceeded 1,000 observations) and the quality (due to limited data, no separation according to more metabolic-related diseases could be done) of the data should be improved.

Prediction of Mineral Composition in Commercial Extruded Dry Dog Food by Near-Infrared Reflectance Spectroscopy

The pet food industry is interested in performing fast analyses to control the nutritional quality of their products. This study assessed the feasibility of near-infrared spectroscopy to predict mineral content in extruded dry dog food. Mineral content in commercial dry dog food samples (n = 119) was quantified by inductively coupled plasma optical emission spectrometry and reflectance spectra (850-2500 nm) captured with FOSS NIRS DS2500 spectrometer. Calibration models were built using modified partial least square regression and leave-one-out cross-validation. The best prediction models were obtained for S (coefficient of determination; R² = 0.89), K (R² = 0.85), and Li (R² = 0.74), followed by P, B, and Sr (R² = 0.72 each). Only prediction models for S and K were adequate for screening purposes. This study supports that minerals are difficult to determine with NIRS if they are not associated with organic molecules.