Human Milk Virome Analysis: Changing Pattern Regarding Mode of Delivery, Birth Weight, and Lactational Stage

Abstract

The human milk (HM) microbiota is a significant source of microbes that colonize the infant gut early in life. The aim of this study was to compare transient and mature HM virome compositions, and also possible changes related to the mode of delivery, gestational age, and weight for gestational age. Overall, in the 81 samples analyzed in this study, reads matching bacteriophages accounted for 79.5% (mainly Podoviridae, Myoviridae, and Siphoviridae) of the reads, far more abundant than those classified as eukaryotic viruses (20.5%, mainly Herpesviridae). In the whole study group of transient human milk, the most abundant families were Podoviridae and Myoviridae. In mature human milk, Podoviridae decreased, and Siphoviridae became the most abundant family. Bacteriophages were predominant in transient HM samples (98.4% in the normal spontaneous vaginal delivery group, 92.1% in the premature group, 89.9% in the C-section group, and 68.3% in the large for gestational age group), except in the small for gestational age group (only ~45% bacteriophages in transient HM samples). Bacteriophages were also predominant in mature HM; however, they were lower in mature HM than in transient HM (71.7% in the normal spontaneous vaginal delivery group, 60.8% in the C-section group, 56% in the premature group, and 80.6% in the large for gestational age group). Bacteriophages still represented 45% of mature HM in the small for gestational age group. In the transient HM of the normal spontaneous vaginal delivery group, the most abundant family was Podoviridae; however, in mature HM, Podoviridae became less prominent than Siphoviridae. Myoviridae was predominant in both transient and mature HM in the premature group (all C-section), and Podoviridae was predominant in transient HM, while Siphoviridae and Herpesviridae were predominant in mature HM. In the small for gestational age group, the most abundant taxa in transient HM were the family Herpesviridae and a species of the genus Roseolovirus. Bacteriophages constituted the major component of the HM virome, and we showed changes regarding the lactation period, preterm birth, delivery mode, and birth weight. Early in life, the HM virome may influence the composition of an infant’s gut microbiome, which could have short- and long-term health implications. Further longitudinal mother–newborn pair studies are required to understand the effects of these variations on the composition of the HM and the infant gut virome.

Optimisation and Application of a Novel Method to Identify Bacteriophages in Maternal Milk and Infant Stool Identifies Host-Phage Communities Within Preterm Infant Gut

“…Specifically, we justify the use of very small sample volumes (as little as 0.1 mL) for very preterm BM phage community characterisation. Previous studies investigating the milk virome have utilized as much as 1.5–10 mL of BM ( 13 – 15 ). Reducing required sample volumes is of particular importance because preterm delivery can have a negative effect on lactogenesis and therefore salvageable volumes can be small to allow as much BM as possible to be available for the infant.…”

“…However, these taxonomic analyses were capped at the family level which limits our ability to determine whether there is a transmission of bacteriophages from mother to infant via BM. A comparison between the virome of BM given to infants delivered at term or preterm found contrasting taxonomic compositions ( 15 ). This study identified several bacteriophage species with host specificity for common skin commensals.…”

The hidden universe of human milk microbiome: origin, composition, determinants, role, and future perspectives

“…However, other studies did not confirm such results [42,43]. A potential influence of the mode of delivery on the virome and mycobiome of HM has been hypothesized as well [44,45].…”

“…Conversely, other authors [42] did not detect any difference in microbial profiles based on length of gestation, postulating a fail-safe mechanism that allows the mother to be "ready" to pass along her bacterial imprint regardless of gestational age at birth, as part of an evolutionary pressure directed towards the baby's benefit. Variations in HM virome and mycobiome composition according to gestational age and birth weight have been recently demonstrated [44,45].…”

“…Some authors [60] observed a relative stability of HMM over time, with only small changes in some minority genera, while others [43] did not observe any effect of lactation stage on HMM composition. Regarding the virome, it was recently documented [44] that, although bacteriophages are predominant in both transient and mature HM samples, transient HM has a greater abundance of Podoviridae and Myoviridae, whereas in mature HM Podoviridae decreases, and Siphoviridae becomes the most abundant family. As for mycobiome, a recent study [45] analyzed samples of HM from different stages of lactation and found that, in transient HM samples, Saccharomyces cerevisiae and Aspergillus glaucus were the most abundant species, while Penicillium rubens and Aspergillus glaucus were predominant in mature HM samples.…”