The human milk microbiome aligns with lactation stage and not birth mode

Safety, Feasibility, and Advantages of Oral Microbiota Transplantation: The First Clinical Case

The pilot clinical study presented demonstrates the possibility, safety, and effectiveness of oral microbiota transplantation from a healthy donor to a patient with neuroblastoma to prevent chemotherapy-induced oral mucositis. A 6-month-old patient with a diagnosis of retroperitoneal neuroblastoma was treated according to the NB 2004 protocol. Due to the development of severe oral mucositis, it was decided to perform oral microbiota transplantation. During the next 3 chemotherapy cycles and conditioning regimen before autologous hematopoietic cell transplantation (auto-HCT), the patient was repeatedly injected per os with donor saliva from her healthy mother. Oral microbiota transplantation was shown to effectively prevent the development of oral mucositis after chemotherapy, and only grade 1 oral mucositis developed after auto-HCT. In all loci of the oral cavity, there was a decreased abundance of bacteria from the Staphylococcaceae, Micrococcaceae, and Xanthomonadaceae families. Conversely, there was an increase in the relative abundance of Streptococcaceae and certain other bacterial taxa. In conclusion, the transplantation of maternal saliva in this patient prevented severe mucositis and was accompanied by a compositional change of the patient's oral microbiota. No adverse events due to the transplantation of maternal saliva were noted.

Metagenomic assessment of the bacterial breastfeeding microbiome in mature milk across lactation

Introduction

Research has illustrated the presence of a diverse range of microbiota in human milk. The composition of the milk microbiome varies across different stages of lactation, emphasizing the need to consider the lactation stage when studying its composition. Additionally, the transfer of both milk and skin microbiota during breastfeeding is crucial for understanding their collective impact on infant health and development. Further exploration of the complete breastfeeding microbiome is necessary to unravel the role these organisms play in infant development. We aim to longitudinally assess the bacterial breastfeeding microbiome across stages of lactation. This includes all the bacteria that infants are exposed to during breastfeeding, such as bacteria found within human milk and any bacteria found on the breast and nipple.

Methods

Forty-six human milk samples were collected from 15 women at 1, 4, 7, and 10 months postpartum. Metagenomic analysis of the bacterial microbiome for these samples was performed by CosmosID (Rockville, MD) via deep sequencing.

Results

Staphylococcus epidermidis and Propionibacteriaceae species are the most abundant bacterial species from these samples. Samples collected at 10 months showed higher abundances of Proteobacteria, Streptococcaceae, Lactobacillales, Streptococcus, and Neisseria mucosa compared to other timepoints. Alpha diversity varied greatly between participants but did not change significantly over time.

Discussion

As the bacterial breastfeeding microbiome continues to be studied, bacterial contributions could be used to predict and reduce health risks, optimize infant outcomes, and design effective management strategies, such as altering the maternal flora, to mitigate adverse health concerns.

Age-specific composition of milk microbiota in Tibetan sheep and goats

This study investigates the dynamic changes in milk nutritional composition and microbial communities in Tibetan sheep and goats during the first 56 days of lactation. Milk samples were systematically collected at five time points (D0, D7, D14, D28, D56) post-delivery. In Tibetan sheep, milk fat, protein, and casein contents were highest on D0, gradually decreased, and stabilized after D14, while lactose and galactose levels showed the opposite trend. Goat milk exhibited similar initial peaks, with significant changes particularly between D0, D7, D14, and D56. 16S rRNA gene sequencing revealed increasing microbial diversity in both species over the lactation period. Principal coordinates analysis identified distinct microbial clusters corresponding to early (D0-D7), transitional (D14-D28), and mature (D56) stages. Core phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, dominated the milk microbiota, with significant temporal shifts. Core microbes like Lactobacillus, Leuconostoc, and Streptococcus were common in both species, with species-specific taxa observed (e.g., Pediococcus in sheep, Shewanella in goats). Furthermore, we observed a highly shared core microbiota in sheep and goat milk, including Lactobacillus, Leuconostoc, and Streptococcus. Spearman correlation analysis highlighted significant relationships between specific microbial genera and milk nutrients. For instance, Lactobacillus positively correlated with total solids, non-fat milk solids, protein, and casein, while Mannheimia negatively correlated with protein content. This study underscores the complex interplay between milk composition and microbial dynamics in Tibetan sheep and goats, informing strategies for livestock management and nutritional enhancement. KEY POINTS: • The milk can be classified into three types based on the microbiota composition • The changes of milk microbiota are closely related to the variations in nutrition • Filter out microbiota with species specificity and age specificity in the milk.

Post Natal Microbial and Metabolite Transmission: The Path from Mother to Infant

The entero-mammary pathway is a specialized route that selectively translocates bacteria to the newborn's gut, playing a crucial role in neonatal development. Previous studies report shared bacterial and archaeal taxa between human milk and neonatal intestine. However, the functional implications for neonatal development are not fully understood due to limited evidence. This study aimed to identify and characterize the microbiota and metabolome of human milk, mother, and infant stool samples using high-throughput DNA sequencing and FT-ICR MS methodology at delivery and 4 months post-partum. Twenty-one mothers and twenty-five infants were included in this study. Our results on bacterial composition suggest vertical transmission of bacteria through breastfeeding, with major changes occurring during the first 4 months of life. Metabolite chemical characterization sheds light on the growing complexity of the metabolites. Further data integration and network analysis disclosed the interactions between different bacteria and metabolites in the biological system as well as possible unknown pathways. Our findings suggest a shared bacteriome in breastfed mother-neonate pairs, influenced by maternal lifestyle and delivery conditions, serving as probiotic agents in infants for their healthy development. Also, the presence of food biomarkers in infants suggests their origin from breast milk, implying selective vertical transmission of these features.

A comparison of the breast milk microbiota from women diagnosed with gestational diabetes mellitus and women without gestational diabetes mellitus

BACKGROUND

Human breast milk (HBM) is a contributing factor in modulating the infant's gut microbiota, as it contains bacteria that are directly transferred to the infant during breastfeeding. It has been shown that children of women diagnosed with gestational diabetes mellitus (GDM) have a different gut microbiota compared to children of women without GDM. Our hypothesis is therefore that women with GDM have a different HBM microbiota, which may influence the metabolic function and capacity of the child later in life. The aim of this study was to investigate whether women with GDM have a different breast milk microbiota 1-3 weeks postpartum compared to women without GDM.

METHODS

In this case-control study, a total of 45 women were included: 18 women with GDM and 27 women without GDM. A milk sample was collected from each participant 1 to 3 weeks postpartum and the bacterial composition was examined by 16 S rRNA gene sequencing targeting the V4 region.

RESULTS

High relative abundances of Streptococcus and Staphylococcus were present in samples from both women with and without GDM. No difference could be seen in either alpha diversity, beta diversity, or specific taxa between groups.

CONCLUSION

Our results did not support the existence of a GDM-associated breast milk microbiota at 1-3 weeks postpartum. Further research is needed to fully understand the development of the gut microbiota of infants born to mothers with GDM.

Comparison of canine colostrum and milk using a multi-omics approach

BACKGROUND

A mother's milk is considered the gold standard of nutrition in neonates and is a source of cytokines, immunoglobulins, growth factors, and other important components, yet little is known about the components of canine milk, specifically colostrum, and the knowledge related to its microbial and metabolic profiles is particularly underwhelming. In this study, we characterized canine colostrum and milk microbiota and metabolome for several breeds of dogs and examined profile shifts as milk matures in the first 8 days post-whelping.

RESULTS

Through untargeted metabolomics, we identified 63 named metabolites that were significantly differentially abundant between days 1 and 8 of lactation. Surprisingly, the microbial compositions of the colostrum and milk, characterized using 16S rRNA gene sequencing, were largely similar, with only two differentiating genera. The shifts observed, mainly increases in several sugars and amino sugars over time and shifts in amino acid metabolites, align with shifts observed in human milk samples and track with puppy development.

CONCLUSION

Like human milk, canine milk composition is dynamic, and shifts are well correlated with developing puppies' needs. Such a study of the metabolic profile of canine milk, and its relation to the microbial community, provides insights into the changing needs of the neonate, as well as the ideal nutrition profile for optimal functionality. This information will add to the existing knowledge base of canine milk composition with the prospect of creating a quality, tailored milk substitute or supplement for puppies.

Mother's Own Milk Versus Donor Human Milk: What's the Difference?

Mother's own milk (MOM) is known to decrease complications in preterm infants and when unavailable, it is recommended that preterm very low-birth weight infants be fed donor human milk (DHM). Due to the pasteurization, processing, and lactation stage of donors, DHM does not contain the same nutritional, immunologic, and microbial components as MOM. This review summarizes the differences between MOM and DHM, the potential effects on health outcomes, and the clinical implications of these differences. Finally, implications for research and clinical practice are discussed.

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.

Microbial Quality of Donkey Milk during Lactation Stages

The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages on the composition and function of donkey milk microbiota. The milk samples were collected at 1, 30, 60, 90, 120, 150, and 180 days post-delivery. The result showed that the microbial composition and functions in donkey milk were significantly affected by different lactation stages. The dominant bacterial phyla in donkey milk are Proteobacteria (60%) and Firmicutes (22%). Ralstonia (39%), Pseudomonas (4%), and Acinetobacter (2%) were the predominant bacterial genera detected in all milk samples. In the mature milk, the abundance of lactic acid bacteria Streptococcus (7%) was higher. Chloroplast (5%) and Rothia (3%) were more plentiful in milk samples from middle and later lactation stages (90-180 d). Furthermore, the pathogens Escherichia-Shigella and Staphylococcus and thermoduric bacteria Corynebacterium, Arthrobacter, and Microbacterium were also detected. Donkey milk is rich in beneficial bacteria and also poses a potential health risk. The above findings have improved our understanding of the composition and function changes of donkey milk microbiota, which is beneficial for the rational utilization of donkey milk.

Unveiling the dynamics of the breast milk microbiome: impact of lactation stage and gestational age

BACKGROUND

Breast milk (BM) provides complete nutrition for infants for the first six months of life and is essential for the development of the newborn's immature immune and digestive systems. While BM was conventionally believed to be sterile, recent advanced high throughput technologies have unveiled the presence of diverse microbial communities in BM. These insights into the BM microbiota have mainly originated from uncomplicated pregnancies, possibly not reflecting the circumstances of mothers with pregnancy complications like preterm birth (PTB).

METHODS

In this article, we investigated the BM microbial communities in mothers with preterm deliveries (before 37 weeks of gestation). We compared these samples with BM samples from healthy term pregnancies across different lactation stages (colostrum, transitional and mature milk) using 16S rRNA gene sequencing.

RESULTS

Our analysis revealed that the microbial communities became increasingly diverse and compositionally distinct as the BM matured. Specifically, mature BM samples were significantly enriched in Veillonella and lactobacillus (Kruskal Wallis; p < 0.001) compared to colostrum. The comparison of term and preterm BM samples showed that the community structure was significantly different between the two groups (Bray Curtis and unweighted unifrac dissimilarity; p < 0.001). Preterm BM samples exhibited increased species richness with significantly higher abundance of Staphylococcus haemolyticus, Propionibacterium acnes, unclassified Corynebacterium species. Whereas term samples were enriched in Staphylococcus epidermidis, unclassified OD1, and unclassified Veillonella among others.

CONCLUSION

Our study underscores the significant influence of pregnancy-related complications, such as preterm birth (before 37 weeks of gestation), on the composition and diversity of BM microbiota. Given the established significance of the maternal microbiome in shaping child health outcomes, this investigation paves the way for identifying modifiable factors that could optimize the composition of BM microbiota, thereby promoting maternal and infant health.

The Impact of the Human Milk Microbiota in the Prevention of Disease and Infant Health

Background: Human milk is recognized as an ideal food for newborns and infants owing to the presence of various nutritive factors, including healthy bacteria. Aim/Objective: This review aimed to understand the effects of human milk microbiota in both the prevention of disease and the health of infants. Methods: Data were obtained from PubMed, Scopus, Web of Science, clinical trial registries, Dergipark, and Türk Atıf Dizini up to February 2023 without language restrictions. Results: It is considered that the first human milk microbiota ingested by the newborn creates the initial microbiome of the gut system, which in turn influences the development and maturation of immunity. Bacteria present in human milk modulate the anti-inflammatory response by releasing certain cytokines, protecting the newborn against certain infections. Therefore, certain bacterial strains isolated from human milk could serve as potential probiotics for various therapeutic applications. Conclusions: In this review, the origin and significance of human milk bacteria have been highlighted along with certain factors influencing the composition of human milk microbiota. In addition, it also summarizes the health benefits of human milk as a protective agent against certain diseases and ailments.

Maternal diet modulates the infant microbiome and intestinal Flt3L necessary for dendritic cell development and immunity to respiratory infection

Poor maternal diet during pregnancy is a risk factor for severe lower respiratory infections (sLRIs) in the offspring, but the underlying mechanisms remain elusive. Here, we demonstrate that in mice a maternal low-fiber diet (LFD) led to enhanced LRI severity in infants because of delayed plasmacytoid dendritic cell (pDC) recruitment and perturbation of regulatory T cell expansion in the lungs. LFD altered the composition of the maternal milk microbiome and assembling infant gut microbiome. These microbial changes reduced the secretion of the DC growth factor Flt3L by neonatal intestinal epithelial cells and impaired downstream pDC hematopoiesis. Therapy with a propionate-producing bacteria isolated from the milk of high-fiber diet-fed mothers, or supplementation with propionate, conferred protection against sLRI by restoring gut Flt3L expression and pDC hematopoiesis. Our findings identify a microbiome-dependent Flt3L axis in the gut that promotes pDC hematopoiesis in early life and confers disease resistance against sLRIs.

The Human Milk Microbiota Produces Potential Therapeutic Biomolecules and Shapes the Intestinal Microbiota of Infants

Human milk not only provides a perfect balance of nutrients to meet all the needs of the infant in the first months of life but also contains a variety of bacteria that play a key role in tailoring the neonatal faecal microbiome. Microbiome analysis of human milk and infant faeces from mother-breastfed infant pairs was performed by sequencing the V1-V3 region of the 16S rRNA gene using the Illumina MiSeq platform. According to the results, there is a connection in the composition of the microbiome in each mother-breastfed infant pair, supporting the hypothesis that the infant's gut is colonised with bacteria from human milk. MiSeq sequencing also revealed high biodiversity of the human milk microbiome and the infant faecal microbiome, whose composition changes during lactation and infant development, respectively. A total of 28 genetically distinct strains were selected by hierarchical cluster analysis of RAPD-PCR (Random Amplified Polymorphic DNA-Polymerase Chain Reaction) electrophoresis profiles of 100 strains isolated from human milk and identified by 16S RNA sequencing. Since certain cellular molecules may support their use as probiotics, the next focus was to detect (S)-layer proteins, bacteriocins and exopolysaccharides (EPSs) that have potential as therapeutic biomolecules. SDS-PAGE (Sodium Dodecyl-Sulfate Polyacrylamide Gel Electrophoresis) coupled with LC-MS (liquid chromatography-mass spectrometry) analysis revealed that four Levilactobacillus brevis strains expressed S-layer proteins, which were identified for the first time in strains isolated from human milk. The potential biosynthesis of plantaricin was detected in six Lactiplantibacillus plantarum strains by PCR analysis and in vitro antibacterial studies. ¹H NMR (Proton Nuclear Magnetic Resonance) analysis confirmed EPS production in only one strain, Limosilactobacillus fermentum MC1. The overall microbiome analysis suggests that human milk contributes to the establishment of the intestinal microbiota of infants. In addition, it is a promising source of novel Lactobacillus strains expressing specific functional biomolecules.

A systematic review of breast milk microbiota composition and the evidence for transfer to and colonisation of the infant gut

The intestinal microbiota plays a major role in infant health and development. However, the role of the breastmilk microbiota in infant gut colonisation remains unclear. A systematic review was performed to evaluate the composition of the breastmilk microbiota and evidence for transfer to/colonisation of the infant gut. Searches were performed using PUBMED, OVID, LILACS and PROQUEST from inception until 18th March 2020 with a PUBMED update to December 2021. 88 full texts were evaluated before final critique based on study power, sample contamination avoidance, storage, purification process, DNA extraction/analysis, and consideration of maternal health and other potential confounders. Risk of skin contamination was reduced mainly by breast cleaning and rejecting the first milk drops. Sample storage, DNA extraction and bioinformatics varied. Several studies stored samples under conditions that may selectively impact bacterial DNA preservation, others used preculture reducing reliability. Only 15 studies, with acceptable sample size, handling, extraction, and bacterial analysis, considered transfer of bacteria to the infant. Three reported bacterial transfer from infant to breastmilk. Despite consistent evidence for the breastmilk microbiota, and recent studies using improved methods to investigate factors affecting its composition, few studies adequately considered transfer to the infant gut providing very little evidence for effective impact on gut colonisation.

Diversity and temporal dynamics of breast milk microbiome and its influencing factors in Chinese women during the first 6 months postpartum

Human breast milk (HBM) plays an important role in providing nutrients, beneficial microorganisms and bioactive components for infants, helping maturation of their immune system and gastrointestinal development. Here, we present a study aiming to investigate the diversity and temporal dynamics of the milk microbiome across the first 6 month postpartum in Chinese healthy breastfeeding women, and to investigate to what extent other variables (e.g., sampling location, infant sex, and mode of delivery) might also be related to variations in the human milk microbiome, and the association with maternal diet and nutrients. Fifty-three healthy pregnant women from four cities were recruited from a China Maternal and Infant Health Cohort Study and breast milk samples were collected and analyzed using 16S rRNA metagenomic sequencing. We illustrated the diversity and temporal dynamics during lactation (Adonis p-value = 3e–04). Firmicutes and Proteobacteria were the most abundant phyla, and Streptococcus, Staphylococcus, Serratia, and Corynebacterium were the core genera. Partitioning around medoids clustering identified two major internal clusters of breast milk microbiota. Cluster 1 was dominated by Acinetobacter and Pseudomonas, while Cluster 2 was dominated by Streptococcus and Staphylococcus. Among other environmental variables, sampling location showed significant influence on breast milk microbiome (Adonis p-value = 4e–04), while infant sex (Adonis p-value = 0.33) and mode of delivery (Adonis p-value = 0.19) were less related to variations in the human milk microbiome. Maternal diet such as tuber was significantly correlated with the relative abundance of Neisseria (rho = 0.34, adjusted p-value = 0.01) and Cutibacterium (rho = −0.35, adjusted p-value = 0.01), and nutrients such as carbohydrates were significantly correlated with the relative abundance of Aquabacterium (rho = −0.39, adjusted p-value = 0.0027), and vitamin B12 was significantly correlated with the relative abundance of Coprococcus (rho = 0.40, adjusted p-value = 0.0018), etc. These results illustrated the dynamic changes of composition and diversity during the lactation phases of the Chinese breast milk microbiome and addressed the importance of geographic location on milk microbiota, and associations with maternal diet consumption, which have potential benefits on the establishment and future health of breastfeeding infants.

The Manifold Bioactivity and Immunoreactivity of Microbial Proteins of Cow and Human Mature Milk in Late Lactation

Simple Summary

The debate over the validity and benefits of breastfeeding children after the age of 1 and the superiority of human over cow’s milk is still ongoing. The recommendation of exclusive breastfeeding for about 6 months, followed by continued breastfeeding as a complementary food source for 1 year or longer, seems justified under many circumstances. The microbiological parameters of the milk play a vital role in this respect. So far, the focus has been on the qualitative profile of the microbiota, bacterial interactions with milk compounds, and the metabolites produced by bacteria. However, the role of bacterial proteins in milk, according to the authors’ knowledge, has been analyzed. It is reported that due to the disruption of the regulatory axis of the immune system in the course of hypersensitivity, organisms may give rise to decreased IgA-mediated (physiological) and increased IgE-mediated (hypersensitive) responses even to host gut microbiota proteins. In this publication, the aim was to compare whether the bacterial proteins in the mature human milk of late lactation and cow’s milk of different breeds can determine the different immunoreactive and bioactive properties of milk.

Abstract

(1) Human milk (HM) is a source of many microorganisms, whose structure contains microbial protein (MP). In addition to the known health-promoting properties of HM, many activities, including immunoreactivity, may result from the presence of MP. Cow’s milk (CM)-derived MP may be 10 times more abundant than MP derived from HM. (2) Raw cow’s milk samples of Holstein and Jersey breeds, commercially available pasteurized milk, and milk from three human donors in the late lactation phase were subjected to chemical and microbiological analyzes. Microorganisms from the milk material were recovered, cultured, and their activities were tested. MPs were extracted and their immunoreactivity was tested with human high IgE pooled sera. The milk types were subjected to simulated digestion. Milk and microbial proteins were identified with LCMS and subjected to an in silico analysis of their activities. Their antioxidant potential was analysed with the DPPH method. (3) The MP of HM shows a stronger IgE and IgG immunoreactivity in the tests with human sera compared to the MP of CM (p = 0.001; p = 0.02, respectively). There were no significant differences between the microbes in the MP of different cattle breeds. The MS-identification and in silico tests of milk and microbial proteins confirmed the presence of MP with immunoreactivity and antioxidant potential. (4) MPs possess a broad bioactive effect, which was determined by an in silico tools. The balance between an MP’s individual properties probably determines the raw material’s safety, which undoubtedly requires further research.

Perspective: Human Milk Composition and Related Data for National Health and Nutrition Monitoring and Related Research

National health and nutrition monitoring is an important federal effort in the United States and Canada, and the basis for many of their nutrition and health policies. Understanding of child exposures through human milk (HM) remains out of reach due to lack of current and representative data on HM's composition and intake volume. This article provides an overview of the current national health and nutrition monitoring activities for HM-fed children, HM composition (HMC) and volume data used for exposure assessment, categories of potential measures in HM, and associated variability factors. In this Perspective, we advocate for a framework for collection and reporting of HMC data for national health and nutrition monitoring and programmatic needs, including a shared vision for a publicly available Human Milk Composition Data Repository (HMCD-R) to include essential metadata associated with HMC. HMCD-R can provide a central, integrated platform for researchers and public health officials for compiling, evaluating, and sharing HMC data. The compiled compositional and metadata in HMCD-R would provide pertinent measures of central tendency and variability and allow use of modeling techniques to approximate compositional profiles for subgroups, providing more accurate exposure assessments for purposes of monitoring and surveillance. HMC and related metadata could facilitate understanding the complexity and variability of HM composition, provide crucial data for assessment of infant and maternal nutritional needs, and inform public health policies, food and nutrition programs, and clinical practice guidelines.

Dynamic Changes in the Human Milk Metabolome Over 25 Weeks of Lactation

Human milk (HM) provides essential nutrition for ensuring optimal infant growth and development postpartum. Metabolomics offers insight into the dynamic composition of HM. Studies have reported the impact of lactation stage, maternal genotype, and gestational age on HM metabolome. However, the majority of the studies have considered changes within the first month of lactation or sampled with large intervals. This leaves a gap in the knowledge of progressing variation in HM composition beyond the first month of lactation. The objective of this study was to investigate whether the HM metabolome from mothers with term deliveries varies beyond 1 month of lactation, during the period in which HM is considered fully mature. Human milk samples (n = 101) from 59 mothers were collected at weeks 1-2, 3-5, 7-9, and 20-25 postpartum and analyzed using 1H nuclear magnetic resonance spectroscopy. Several metabolites varied over lactation and exhibited dynamic changes between multiple time points. Higher levels of HM oligosaccharides, cis-aconitate, O-phosphocholine, O-acetylcarnitine, gluconate, and citric acid were observed in early lactation, whereas later in lactation, levels of lactose, 3-fucosyllactose, glutamine, glutamate, and short- and medium-chain fatty acids were increased. Notably, we demonstrate that the HM metabolome is dynamic during the period of maturity.

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.