The gut virome of healthy children during the first year of life is diverse and dynamic.
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ABSTRACT:
SUBMITTER: Taboada B
PROVIDER: S-EPMC8046192 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe early life of the human host marks a critically important time for establishment of the gut microbial community, yet the developmental trajectory of gut community-encoded resistance genes (resistome) is unknown. We present a longitudinal study of the fecal antibiotic resistome of healthy amoxicillin-exposed and antibiotic-naive twins and their mothers during the first year of life.ResultsWe extracted metagenomic DNA (mgDNA) from fecal samples collected from three healthy twin pairs at three timepoints (1 or 2 months, 6 or 7 months, and 11 months) and from their mothers (collected at delivery). The mgDNA was used to construct metagenomic expression libraries in an Escherichia coli host. These libraries were screened for antibiotic resistance, and functionally selected resistance genes were sequenced and annotated. A diverse fecal resistome distinct from the maternal resistome was apparent by 2 months of age, and infants' fecal resistomes included resistance to clinically important broad-spectrum beta-lactam antibiotics (e.g., piperacillin-tazobactam, aztreonam, cefepime) not found in their mothers. Dissemination of resistance genes among members of a given family was positively correlated with sharing of those same resistance genes between unrelated families, potentially identifying within-family sharing as a marker of resistance genes emerging in the human community at large. Finally, we found a distinct developmental trajectory for a community-encoded function: chloramphenicol resistance. All study subjects at all timepoints harbored chloramphenicol resistance determinants, but multidrug efflux pumps (rarely found in mothers) were the primary effectors of chloramphenicol resistance in young infants. Chloramphenicol acetyltransferases were more common in mothers than in infants and were found in nearly all the infants at later timepoints.ConclusionsOur results suggest that healthy 1-2-month-old infants' gut microbes harbor clinically relevant resistance genes distinct from those of their mothers, and that family-specific shared environmental factors early in life shape resistome development.
| S-EPMC4480905 | biostudies-literature
Project description:ObjectivesThe purpose of this study was to quantify the symmetry of the alveolar process of the maxilla and palate during the first year of life in healthy infants with the help of a semiautomatic segmentation technique.Materials and methodsMaxillary plaster models of seventy healthy babies at 0, 3, 6, 9, and 12 months were collected and digitized. A semiautomatic segmentation tool was used to extract the alveolus and palate. The resulting model was aligned within a reference frame and mirrored on its medial plane. Distance maps were created and analyzed to compare and quantify the differences between the two hemispheres. Additional hemispherical width and area measurements were performed. An ANOVA test with additional post hoc tests was performed to check if the symmetry changed during development. Finally, the results were tested on intra- and interobserver variability.ResultsThe absolute mean inter-surface distance between the original and mirrored models in each age group ranged between 0.23 and 0.30 mm. Width and area analysis showed a small but significant larger left palatal hemisphere. ANOVA and post hoc tests showed no significant difference in symmetry between groups. Reliability analysis showed no significant differences between observers.ConclusionsThis study showed that in this infant population, only a small degree of palatal asymmetry was present, which can be considered as normal and clinically irrelevant.Clinical relevanceThe data from this study can be used in future comparative studies as reference data. Furthermore, modeling of these data can help in predicting the growth pattern, which may lead to improved treatment protocols for children with craniofacial anomalies.
| S-EPMC7878251 | biostudies-literature
Project description:The gut microbiota is involved in the production of numerous metabolites that maintain host wellbeing. The assembly of the gut microbiome is highly dynamic, and influenced by many postnatal factors, moreover, little is known about the development of the gut metabolome. We showed that geography has an important influence on the microbiome dynamics in the first year of life based on two independent cohorts from China and Sweden. Major compositional differences since birth were the high relative abundance of Bacteroides in the Swedish cohort and Streptococcus in the Chinese cohort. We analyzed the development of the fecal metabolome in the first year of life in the Chinese cohort. Lipid metabolism, especially acylcarnitines and bile acids, was the most abundant metabolic pathway in the newborn gut. Delivery mode and feeding induced particular differences in the gut metabolome since birth. In contrast to C-section newborns, medium- and long-chain acylcarnitines were abundant at newborn age only in vaginally delivered infants, associated by the presence of bacteria such as Bacteroides vulgatus and Parabacteroides merdae. Our data provide a basis for understanding the maturation of the fecal metabolome and the metabolic role of gut microbiota in infancy.
| S-EPMC10334852 | biostudies-literature
Project description:The human gut microbiota plays a vital role in health and disease, and microbial colonization is a key process in infant development. Here, we analyze 2684 fecal specimens from 12 infants during their first year of life, providing detailed insights into the human gut colonization process. Maturation of the gut microbial community shows strong temporal structure and specific developmental stages. At 2-4 months of age, there is a period of accelerated convergence concurrent with a bloom of Bifidobacterium, a genus associated with metabolism of oligosaccharides found in breast milk. The end of this period coincides with the introduction of solid food, a reduction in the relative abundance of Bifidobacterium, and an increase in several groups of Firmicutes. Our findings highlight the dynamic nature and individuality of the gut colonization process, and the need for high-frequency sampling over an extended period when designing and interpreting infant microbiome studies.
| S-EPMC5993781 | biostudies-literature
Project description:BackgroundThe relationship between the gut microbiome and the human host is dynamic and we may expect adjustments in microbiome function if host physiology changes. Metatranscriptomic approaches should be key in unraveling how such adjustments occur.MethodsWe employ metatranscriptomic sequencing analyses to study gene expression in the gut microbiota of infants through their first year of life, and of their mothers days before delivery and one year afterwards.FindingsIn infants, hallmarks of aerobic metabolism disappear from the microbial metatranscriptome as development proceeds, while the expression of functions related to carbohydrate transport and metabolism increases and diversifies, approaching that observed in non-pregnant women. Butyrate synthesis enzymes are overexpressed at three months of age, even though most butyrate-producing organisms are still rare. In late pregnancy, the microbiota readjusts the expression of carbohydrate-related functions in a manner consistent with a high availability of glucose.InterpretationOur findings suggest that butyrate production may be ensured in the gut of young infants before the typical butyrate synthesizers of the adult gut become abundant. The late pregnancy gut microbiota may be able to access the high levels of blood glucose characteristic of this period. Moreover, late pregnancy gut bacteria may reach stationary phase, which may affect their likelihood of translocating across the intestinal epithelium.FundsThis work was supported by grants CSD2009-00006 (CONSOLIDER Program) and SAF2009-13032-C02-02 from MICINN (Ministry of Science and Innovation, Spain), and by grant SAF2012-31187 from MINECO (Ministry of Economics and Competitiveness, Spain).
| S-EPMC6354444 | biostudies-literature
Project description:BackgroundThe objective of this study was to characterize longitudinal colonization with Streptococcus pneumoniae during the first year of life within a community newborn infant cohort, and assess the relationship between antibiotic exposure and colonization with antibiotic-resistant organisms.MethodsDuring April 2013-February 2014, 326 infants were enrolled from an urban academic hospital well-baby nursery. At ages 4, 8, and 12 months, we collected antibiotic data, other exposure data, and nasopharyngeal cultures for pneumococcal isolation.ResultsFollow-up visits were completed for 211, 158, and 144 infants at ages 4, 8, and 12 months, respectively. By 12 months, 33% of infants attending the visits had ever been exposed to antibiotics, 67% if exposures to maternal antibiotics at birth are included. Pneumococci were isolated at 38/839 (4.5%) visits from 38 infants, including one 13-valent conjugate vaccine (PCV13) serotype (6A). There were 1 (0.3%), 15 (7%), 7 (4%), and 15 (10%) infants who were colonized at 0-, 4-, 8-, and 12-month visits, respectively. By age 12 months, at least 35 (11%) infants had ever been colonized. Sixteen isolates (42%) exhibited nonsusceptibility to at least 1 antibiotic. Infants with recent antibiotic exposure were not more likely to be colonized or to harbor nonsusceptible organisms.ConclusionsWithin a hospital birth cohort followed in the community, pneumococcal colonization and related antibiotic resistance were lower than previously reported, likely associated with PCV13 use. Antibiotic exposure was not associated with subsequent colonization with resistant isolates. The influence of other environmental factors needs further study.
| S-EPMC7495909 | biostudies-literature
Project description:Traditional culture techniques have shown that increased bacterial colonization is associated with viral colonization; however, the influence of viral colonization on the whole microbiota composition is less clear. We thus aimed to understand the interaction of viral infections and the nasal microbiota in early life to appraise their roles in disease development. Thirty-two healthy, unselected infants were included in this prospective longitudinal cohort study within the first year of life. Biweekly nasal swabs (n = 559) were taken, and the microbiota was analyzed by 16S rRNA pyrosequencing, and 10 different viruses and 2 atypical bacteria were characterized by real-time PCR (combination of seven duplex samples). In contrast to asymptomatic human rhinovirus (HRV) colonization, symptomatic HRV infections were associated with lower alpha diversity (Shannon diversity index [SDI]), higher bacterial density (PCR concentration), and a difference in beta diversities (Jaccard and Bray-Curtis index) of the microbiota. In addition, infants with more frequent HRV infections had a lower SDI at the end of the study period. Overall, changes in the microbiota associated with symptomatic HRV infections were characterized by a loss of microbial diversity. The interaction between HRV infections and the nasal microbiota in early life might be of importance for later disease development and indicate a potential approach for future interventions. IMPORTANCE Respiratory viral infections are very frequent in infancy and of importance in acute and chronic disease development. Infections with human rhinovirus (HRV) are, e.g., associated with the later development of asthma. We found that only symptomatic HRV infections were associated with acute changes in the nasal microbiota, mainly characterized by a loss of microbial diversity. Infants with more frequent symptomatic HRV infections had a lower bacterial diversity at the end of the first year of life. Whether the interaction between viruses and the microbiota is one pathway contributing to asthma development will be assessed in the follow-ups of these children. Independent of that, measurements of microbial diversity might represent a potential marker for risk of later lung disease or monitoring of early life interventions.
| S-EPMC5120172 | biostudies-literature
Project description:Three-dimensional (3D) surface imaging systems are replacing direct anthropometry as the preferred method for capturing facial soft-tissues. Aims of this study were: (1) to develop normative average 3D faces of healthy infants aged 3, 6, 9, and 12 months and (2) to describe normative average 3D facial growth data in infants aged 3 to 12 months. Three-dimensional images of 50 healthy children were acquired at 3, 6, 9, and 12 months of age using the 3dMDcranial system. Four average faces with uniform meshes (3, 6, 9, and 12 months) were developed and registered based on the children's reference frames. Distance maps of growth of the total facial surface and of the nose, upper lip, chin, forehead and cheeks for the intervals 3 to 6 months, 6 to 9 months, and 9 to 12 months of age were calculated. Mean growth of the total facial surface was 3.9 mm (standard deviation [SD] 1.2 mm), 3.5 mm (SD 0.9 mm), and 1.6 mm (SD 0.7 mm) at 3 to 6 months, 6 to 9 months, and 9 to 12 months, respectively. Regarding the selected regions of the face, the mean growth of the nose and upper lip were the largest (3.7 mm and 3.6 mm, respectively) between 6 and 9 months of age. The mean growth of the forehead, cheeks and chin were the largest (5.4 mm, 3.2, and 4.7 mm, respectively) between 3 and 6 months of age. For all facial regions, growth clearly diminished from 9 to 12 months of age. Normative data on the growth of the full face, nose, upper lip, chin, forehead and cheeks are presented. Such data can be used in future studies to identify the effectiveness of treatment of orofacial deformities such as orofacial clefts during the first year of life.
| S-EPMC6527206 | biostudies-literature
Project description:Plant viruses have been reported to be common in the gut of human adults, presumably as result of food ingestion. In this work, we report that plant viruses can also be found frequently in the gut and oropharynx of children during their first year of life, even when they are exclusively breast-fed. Fecal and oropharynx samples were collected monthly, from birth to 1 year of age, from three apparently healthy children in a semi-rural community and analyzed by next generation sequencing. In 100% of the fecal samples and 65% of the oropharynx samples at least one plant virus was identified. Tobamoviruses in the Virgaviridae family were by far the most frequently detected, with tropical soda apple mosaic virus, pepper mild mottle virus, and opuntia tobamovirus 2 being the most common species. Seventeen complete virus genomes could be assembled, and phylogenetic analyses showed a large diversity of virus strains circulating in the population. These results suggest that children are continuously exposed to an extensive and highly diverse collection of tobamoviruses. Whether the common presence of plant viruses at an early age influences the infant's immune system, either directly or through interaction with other members of the microbiota, remains to be investigated.
| S-EPMC7423923 | biostudies-literature
Project description:HIV-exposed uninfected infants (HEU) have abnormal immunologic functions and increased infectious morbidity in the first 6 months of life, which gradually decreases thereafter. The mechanisms underlying HEU immune dysfunctions are unknown. We hypothesized that unique characteristics of the HEU gut microbiota associated with maternal HIV status may underlie the HEU immunologic dysfunctions. We characterized the infant gut, maternal gut, and breast milk microbiomes of mother-infant pairs, including 123 with HEU and 117 with HIV-uninfected infants (HUU), from South Africa. Pan-bacterial 16S rRNA gene sequencing was performed on (i) infant stool at 6, 28, and 62 weeks; (ii) maternal stool at delivery and 62 weeks; and (iii) breast milk at 6 weeks. Infant gut alpha and beta diversities were similar between groups. Microbial composition significantly differed, including 12 genera, 5 families and 1 phylum at 6 weeks; 12 genera and 2 families at 28 weeks; and 2 genera and 2 families at 62 weeks of life. Maternal gut microbiomes significantly differed in beta diversity and microbial composition, and breast milk microbiomes differed in microbial composition only. Infant gut microbiotas extensively overlapped with maternal gut and minimally with breast milk microbiotas. Nevertheless, exclusively breastfed HEU and HUU had less divergent microbiomes than nonexclusively breastfed infants. Feeding pattern and maternal gut microbiome imprint the HEU gut microbiome. Compared to HUU, the HEU gut microbiome prominently differs in early infancy, including increased abundance of taxa previously observed to be present in excess in adults with HIV. The HEU and HUU gut microbiome compositions converge over time, mirroring the kinetics of HEU infectious morbidity risk. IMPORTANCE HIV-exposed uninfected infants (HEU) are highly vulnerable to infections in the first 6 months of life, and this vulnerability decreases to the age of 24 months. Because the microbiome plays a critical role in the education of the infant immune system, which protects them against infections, we characterized the gut microbiomes of HEU and HIV-unexposed infants (HUU) in the first year of life. The HEU and HUU gut microbiomes showed prominent differences at 6 and 28 weeks of life but converged at 62 weeks of life, mirroring the time course of the HEU excess infectious morbidity and suggesting a potential association between the infant gut microbiome structure and susceptibility to infections. Infant gut microbiotas extensively overlapped with maternal gut and minimally with breast milk microbiotas. Moreover, exclusively breastfed HEU and HUU had less divergent microbiomes at 6 and 28 weeks than nonexclusively breastfed HEU and HUU. The factors that affect the HEU gut microbiome, maternal gut microbiome and exclusive breastfeeding, may be targeted by interventions.
| S-EPMC9600264 | biostudies-literature