Longitudinal comparison of the developing gut virome in infants and their mothers

Walters, William A.; Granados, Andrea; Ley, Catherine; Federman, Scot; Stryke, Doug; Santos, Yale A.; Haggerty, Thomas D.; Sotomayor-González, Alicia; Servellita, Venice; Ley, Ruth E.; Parsonnet, Julie; Chiu, Charles Y.

doi:10.1016/j.chom.2023.01.003

Cited by 23 publications

(19 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1A). This differs from some previous studies which report decreasing bacteriophage diversity over the first few years of life, possibly due to differences in preparation of the samples and updated bioinformatics tools and databases utilized in our study [15,21]. However other reports concur with our study and show an increasing diversity of bacteriophages in infancy [22,23].…”

Section: Resultscontrasting

confidence: 99%

“…The reasons for the difference in bacteriophage colonization and function by delivery mode up to 24 months is still yet to be determined. While differential acquisition of the maternal virome is possible, as infants delivered by CS bypass the birth canal and maternal vaginal and perineal microbiome exposure, studies suggest that maternal to infant transmission of the virome in early life is already very low [14, 15]. It has been suggested dietary factors such as breastfeeding contribute to early life virome colonization, however there were no differences in breastfeeding by delivery mode in our study (Table S1).…”

Section: Resultsmentioning

confidence: 56%

“…Although gut bacteriophages can alter microbiome composition and function and directly affect host immune responses [10][11][12][13], the effect of delivery mode has largely been limited to investigation of bacterial taxa. Transmission of the gut virome from mother to infant has shown lower transmission of viral communities than bacterial communities, and that virome colonization was determined more by dietary and environmental factors rather than direct maternal acquisition [14,15]. In the first week of life, delivery mode did not determine how much of the virome was shared between mother and infant but some effect of delivery mode on bacteria-bacteriophage interaction was seen [14].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Delivery mode impacts gut bacteriophage colonization during infancy

Subramanian,

Romero-Soto,

Stern

et al. 2023

Preprint

View full text Add to dashboard Cite

BackgroundCesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory and immune health outcomes. Although gut bacteriophages can alter gut microbiome composition and impact host immune responses, little is known about how delivery mode impacts bacteriophage colonization over time. To begin to address this we examined how delivery mode affected bacteriophage colonization over the first two years of life.ResultsShotgun metagenomic sequencing was conducted on 272 serial stool samples from 55 infants, collected at 1-2 days of life and 2, 6, 12 and 24 months. 33/55 (60%) infants were born by vaginal delivery. DNA viruses were identified, and by host inference, 94% of the viral sequences were found to be bacteriophages. Alpha diversity of the virome was increased in vaginally delivered infants compared to cesarean section delivered infants at 2 months (Shannon index, p=0.022). Beta diversity significantly differed by delivery mode at 2, 6, and 12 months when stratified by peripartum antibiotic use (Bray–Curtis dissimilarity, all p<0.05). Significant differentially abundant predicted bacteriophage hosts by delivery mode were seen at all time points. Moreover, there were differences in predicted bacteriophage functional gene abundances up to 24 months by delivery mode. Many of the functions considered to play a role in host response were increased in vaginal delivery.ConclusionsClear differences in bacteriophage composition and function were seen by delivery mode over the first two years of life. Given that phages are known to affect host immune response, our results suggest that future investigation into how delivery mode may lead to adverse inflammatory outcomes should not only include bacterial microbial colonization but also the potential role of bacteriophages and transkingdom interactions.

show abstract

Section: Resultscontrasting

confidence: 99%

Section: Resultsmentioning

confidence: 56%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Delivery mode impacts gut bacteriophage colonization during infancy

Subramanian,

Romero-Soto,

Stern

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Additionally, the Pseudomonas phage Φ6 was chosen to represent enveloped dsRNA phages. Although enveloped dsRNA phages are less commonly detected natively in the human gut microbiome [30,2], environmental and human RNA viruses are often present and could be important to the overall virome composition and activity as well as host health [31]. The individual phages were mixed just before use to generate the phage mock community.…”

Section: Phage Mock Communitymentioning

confidence: 99%

Choice of Ultrafilter affects Recovery Rate of Bacteriophages

Larsen,

Offersen,

et al. 2023

Preprint

View full text Add to dashboard Cite

Studies into the viral fraction of the microbiota have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from samples, and the protocols that exist are fraught with procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of basic filtering of macromolecules and bacteria, yet even this affects the viruses in a strain-specific manner. In this study we investigate a protocol for viral extraction based on ultrafiltration and how the choice of ultrafilter might influence the viral community. Especially the enveloped F6 phage is severely affected by choice of filter, but also tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We postulate that the cause of this bias might be the retention of bacterial debris capable of inactivating specific phages in filters with smaller pore sizes, suggesting the need for greater thought when selecting filters for virus extraction.

show abstract

“…The few attempts that have characterized the gut virome early in life have revealed that its composition is highly dynamic [26][27][28] , affected by delivery mode 6 and the first bacterial colonizers 29 as well as being enriched in phages belonging to the Microviridae family 10,27 . Moreover, its transmission-dynamics after birth follows a stepwise assembly, with breastfeeding playing a protective role against eukaryotic viral infections 30,31 . Understanding how environmental exposures and phenotypes intertwine the vector space conformed by viruses, bacteria, host, and their functional attributes remains an unsolved task.…”

Section: Introductionmentioning

confidence: 99%

The influence of early life exposures on the infant gut virome

Zhang

Castro‐Mejía

Deng

et al. 2023

Preprint

View full text Add to dashboard Cite

SummaryLarge cohort studies have contributed significantly to our understanding of the factors that influence the development of the bacterial component of the gut microbiome (GM) during the first years of life. However, the factors that shape the colonization by other important GM members such as the viral fraction remain more elusive. Most gut viruses are bacteriophages (phages), i.e., viruses attacking bacteria in a host specific manner, and to a lesser extent, but also widely present, eukaryotic viruses, including viruses attacking human cells. Here, we utilize the deeply phenotyped COPSAC2010 birth cohort consisting of 700 infants to investigate how social, pre-, peri- and postnatal factors may influence the gut virome composition at one year of age, where fecal virome data was available from 645 infants.Among the different exposures studied, having older siblings and living in an urban vs. rural area had the strongest impact on gut virome composition. Differential abundance analysis from a total of 16,118 viral operational taxonomic units (vOTUs) (mainly phages, but also 6.1% eukaryotic viruses) identified 2,105 vOTUs varying with environmental exposures, of which 5.9% were eukaryotic viruses and the rest was phages. Bacterial hosts for these phages were mainly predicted to be within theBacteroidaceae, Prevotellaceae, andRuminococcaceaefamilies, as determined by CRISPR spacer matches. Spearman correlation coefficients indicated strong co-abundance trends of vOTUs and their targeted bacterial host, which underlined the predicted phage-host connections. Further, our findings show that some gut viruses encode important metabolic functions and how the abundance of genes encoding these functions is influenced by environmental exposures. Genes that were significantly associated with early life exposures were found in a total of 42 vOTUs. 18 of these vOTUs had their life styles predicted, with 17 of them having a temperate lifestyle. These 42 vOTUs carried genes coding for enzymes involved in alanine, aspartate and glutamate metabolism, glycolysis-gluconeogenesis, as well as fatty acid biosynthesis. The latter implies that these phages could be involved in the utilization and degradation of major dietary components and affect infant health by influencing the metabolic capacity of their bacterial host.Given the importance of the GM in early life for maturation of the immune system and maintenance of metabolic health, these findings provide a valuable source of information for understanding early life factors that predispose for autoimmune and metabolic disorders.

show abstract

Longitudinal comparison of the developing gut virome in infants and their mothers

Cited by 23 publications

References 40 publications

Delivery mode impacts gut bacteriophage colonization during infancy

Delivery mode impacts gut bacteriophage colonization during infancy

Choice of Ultrafilter affects Recovery Rate of Bacteriophages

The influence of early life exposures on the infant gut virome

Contact Info

Product

Resources

About