The Influence of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing

The role of antibiotic exposure and the effects of breastmilk and human milk feeding on the developing infant gut microbiome

The World Health Organization (WHO) recommends exclusive breastfeeding for the first 6 months of life followed by complementary foods and sustained breastfeeding for at least 2 years, underscoring its pivotal role in reducing infant mortality and preventing various illnesses. This perspective delves into the intricate relationship between breastfeeding practices, early life antibiotic exposure, and infant gut microbiome development, highlighting their profound influence on child health outcomes. Antibiotics are extensively prescribed during pregnancy and childhood, disrupting the microbiome, and are related to increased risks of allergies, obesity, and neurodevelopmental disorders. Breastfeeding is a significant determinant of a healthier gut microbiome, characterized by higher levels of beneficial bacteria such as Bifidobacterium and lower levels of potential pathogens. Despite widespread recognition of the benefits of breastfeeding, gaps persist in healthcare practices and support mechanisms, exacerbating challenges faced by breastfeeding families. This highlights the pressing need for comprehensive research encompassing breastfeeding behaviors, human milk intake, and their impact on infant health outcomes. Additionally, promoting awareness among healthcare providers and families regarding the detrimental effects of unnecessary formula supplementation could facilitate informed decision-making and bolster exclusive breastfeeding rates. Moreover, donor human milk (DHM) is a promising alternative to formula, potentially mitigating disruptions to the infant gut microbiome after antibiotic exposure. Overall, prioritizing breastfeeding support interventions and bridging research gaps are essential steps towards improving child health outcomes on a global scale.

The preterm human milk microbiota fluctuates by postpartum week and is characterized by gestational age and maternal BMI

IMPORTANCE

Despite a growing recognition that the type of nutrition received by preterm infants influences their intestinal microbiome and health outcomes, the microbiota of mother's own milk (MOM), pasteurized donor human milk (PDHM), and infant formula remain poorly characterized. In our study, we found that the structure of microbial communities, bacterial diversity, and relative abundances of specific genera were significantly different between MOM, PDHM, and formula. Additionally, our results suggest that the microbiota of MOM changes as a function of time and maternal factors. Lastly, we identified three lactotypes within MOM that have distinct microbial compositions and described the maternal factors associated with them. These findings set the stage for future research aimed at advancing our knowledge of the microbiota of preterm infant nutrition and the specific influence it may have on health outcomes.

Metagenomic, microbiological, chemical and sensory profiling of Caciocavallo Podolico Lucano cheese

In this study, Caciocavallo Podolico Lucano (CPL) cheese was deeply characterized for its bacterial community, chemical composition and sensory aspects. The entire cheese making process (from milk collection to ripened cheese) was performed by strictly applying the traditional protocol for CPL production in four dairy factories (A-D) representative of the production area. The vat made of wood represents the main transformation tool for CPL cheese production and the biofilms hosted onto the internal surfaces of all vats analyzed in this study were dominated by lactic acid bacteria. Total mesophilic microorganisms present in bulk milk (4.7-5.0 log CFU/ml) increased consistently after contact with the wooden vat surfaces (5.4-6.4 log CFU/ml). The application of Illumina sequencing technology identified barely 18 taxonomic groups among processed samples; streptococci and lactobacilli constituted the major groups of the wooden vat biofilms [94.74-99.70 % of relative abundance (RA)], while lactobacilli dominated almost entirely (94.19-100 % of total RA) the bacterial community of ripened cheeses. Except coagulase positive staphylococci, undesirable bacteria were undetectable. Among chemical parameters, significant variations were registered for unsaturated, monounsaturated, polyunsaturated fatty acids and antioxidant properties (significantly lower for CPL cheeses produced in factory B). The cheeses from factories A, C and D were characterized by a higher lactic acid and persistence smell attributes than factory B. This work indicated that the strict application of CPL cheese making protocol harmonized the main microbiological, physicochemical and sensory parameters of the final cheeses produced in the four factories investigated.

A Pilot Study on Donor Human Milk Microbiota: A Comparison with Preterm Human Milk Microbiota and the Effect of Pasteurization

Human milk (HM) is the best feeding option for preterm infants; however, when mother’s own milk (MOM) is not available, pasteurized donor human milk (DHM) is the best alternative. In this study, we profiled DHM microbiota (19 samples) using 16S rRNA amplicon sequencing and compared its compositional features with the MOM microbiota (14 samples) from mothers who delivered prematurely (PT-MOM). As a secondary study aim, we assessed the specific effect of pasteurization on the characteristics of the DHM microbiota. DHM showed significantly higher alpha diversity and significant segregation from PT-MOM. Compositionally, the PT-MOM microbiota had a significantly higher proportion of Staphylococcus than DHM, with Streptococcus tending to be and Pseudomonas being significantly overrepresented in DHM compared with the PT-MOM samples. Furthermore, pasteurization affected the HM microbiota structure, with a trend towards greater biodiversity and some compositional differences following pasteurization. This pilot study provided further evidence on the HM microbial ecosystem, demonstrating that the DHM microbiota differs from the PT-MOM microbiota, possibly due to inherent differences between HM donors and mothers delivering prematurely, and that pasteurization per se impacts the HM microbiota. Knowledge about HM microbiota needs to be acquired by investigating the effect of DHM processing to develop strategies aimed at improving DHM quality while guaranteeing its microbiological safety.

Detection and Quantification of Immunoregulatory miRNAs in Human Milk and Infant Milk Formula

Mammary gland secretory cells produce miRNA-rich milk. In humans, these miRNAs reach infant/neonate bloodstream, playing diverse roles, like neural system development, metabolism, and immune system maturation. Notwithstanding, still few works explore human milk miRNA content, and there are no reports at the population level. Our hypothesis was that miR-146b-5p, miR148a-3p, miR155-5p, mir181a-5p, and mir200a-3p immunoregulatory miRNAs are expressed in human colostrum/milk at a higher level than infant milk formulae. The aim of this work was to evaluate the expression of the five immunoregulatory miRNAs in human milk and compare it with their expression in infant milk formula. For this purpose, miRNA relative expression was measured by qPCR in cDNA prepared from total RNA extracted from sixty human colostrum/milk samples and six different formulae. The comparative Cт method 2^−ΔCт using exogenous cel-miR-39 as internal control was employed, followed by statistical analysis. We found the relative expression levels of miRNAs are comparable among colostrum/milk samples, and these miRNAs are present in infant milk formulae but at very low concentrations. We conclude that the relative expression of the immunomodulatory miRNAs is comparable in all the human colostrum/milk samples and is higher than the expression in formulae.

Inoculation of mother's own milk could personalize pasteurized donor human milk used for feeding preterm infants

BACKGROUND

Human milk is a vehicle for bioactive compounds and beneficial bacteria which promote the establishment of a healthy gut microbiome of newborns, especially of preterm infants. Pasteurized donor human milk (PDHM) is the second-best option when preterm mother's own milk is unavailable. Since pasteurization affect the microbiological quality of donor milk, PDHM was inoculated with different preterm milk samples and then incubated, in order to evaluate the effect in terms of bacterial growth, human milk microbiome and proteolytic phenomena.

METHODS

In an in-vitro study PDHM was inoculated at 10% v/v using ten preterm milk samples. Microbiological, metataxonomic and peptidomic analyses, on preterm milk samples at the baseline (T0), on PDHM and on inoculated milk (IM) samples at T0, after 2 h (T1) and 4 h (T2) of incubation at 37 °C, were conducted.

RESULTS

IM samples at T2 showed a Total Bacterial Count not significantly different (p > 0.01) compared to preterm milk samples. At T2 lactic acid bacteria level was restored in all IM. After inoculation, metataxonomic analysis in IM samples showed that Proteobacteria remained the predominant phylum while Firmicutes moved from 3% at T1 to 9.4% at T2. Peptidomic profile of IM resembled that of PDHM, incubated for the same time, in terms of number and type of peptides.

CONCLUSION

The study demonstrated that inoculation of PDHM with mother's own milk could restore bacterial growth and personalize human milk microbiome in PDHM. This effect could be beneficial because of the presence of maternal probiotic bacteria which make PDHM more similar to mother's own milk.

The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota

Research investigating the gut microbiome (GM) during a viral infection may necessitate inactivation of the fecal viral load. Here, we assess how common viral inactivation techniques affect 16S rRNA-based analysis of the gut microbiome. Five common viral inactivation methods were applied to cross-matched fecal samples from sixteen female CD-1 mice of the same GM background prior to fecal DNA extraction. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA. Treatment-dependent effects on DNA yield, genus-level taxonomic abundance, and alpha and beta diversity metrics were assessed. A sodium dodecyl sulfate (SDS)-based inactivation method and Holder pasteurization had no effect on measures of microbial richness, while two Buffer AVL-based inactivation methods resulted in a decrease in detected richness. SDS inactivation, Holder pasteurization, and the AVL-based inactivation methods had no effect on measures of alpha diversity within samples or beta diversity between samples. Fecal DNA extracted with TRIzol-treated samples failed to amplify and sequence, making it unsuitable for microbiome analysis. These results provide guidance in the 16S rRNA microbiome analysis of fecal samples requiring viral inactivation.