Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States.
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ABSTRACT:
SUBMITTER: Casaburi G
PROVIDER: S-EPMC7820601 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal-infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R2 = 0.038), this was not true for neonatal stool (meconium; Mann-Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode. For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R2 = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes substantial reorganization, which is primarily driven by body site and not by mode of delivery.
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Project description:The rumen hosts one of the most efficient microbial systems for degrading plant cell walls, yet the predominant cellulolytic proteins and fibrolytic mechanism(s) remain elusive. Here we investigated the cellulolytic microbiome of the yak rumen by using a combination of metagenome-based and bacterial artificial chromosome (BAC)-based functional screening approaches. Totally 223 fibrolytic BAC clones were pyrosequenced and 10,070 ORFs were identified. Among them 150 were annotated as the glycoside hydrolase (GH) genes for fibrolytic proteins, and the majority (69%) of them were clustered or linked with genes encoding related functions. Among the 35 fibrolytic contigs of >10 Kb in length, 25 were derived from Bacteroidetes and four from Firmicutes. Coverage analysis indicated that the fibrolytic genes on most Bacteroidetes-contigs were abundantly represented in the metagenomic sequences, and they were frequently linked with genes encoding SusC/SusD-type outer-membrane proteins. GH5, GH9, and GH10 cellulase/hemicellulase genes were predominant, but no GH48 exocellulase gene was found. Most (85%) of the cellulase and hemicellulase proteins possessed a signal peptide; only a few carried carbohydrate-binding modules, and no cellulosomal domains were detected. These findings suggest that the SucC/SucD-involving mechanism, instead of one based on cellulosomes or the free-enzyme system, serves a major role in lignocellulose degradation in yak rumen. Genes encoding an endoglucanase of a novel GH5 subfamily occurred frequently in the metagenome, and the recombinant proteins encoded by the genes displayed moderate Avicelase in addition to endoglucanase activities, suggesting their important contribution to lignocellulose degradation in the exocellulase-scarce rumen.
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Project description:Host-associated microbiomes can play key roles in the metamorphosis of animals. Most scyphozoan jellyfish undergo strobilation in their life cycles, similar to metamorphosis in classic bilaterians. The exploration of jellyfish microbiomes may elucidate the ancestral mechanisms and evolutionary trajectories of metazoan-microbe associations and interactions during metamorphosis. However, current knowledge of the functional features of jellyfish microbiomes remains limited. Here, we performed a genome-centric analysis of associated microbiota across four successive life stages (polyp, early strobila, advanced strobila, and ephyra) during strobilation in the common jellyfish Aurelia coerulea. We observed shifts in taxonomic and functional diversity of microbiomes across distinct stages and proposed that the low microbial diversity in ephyra stage may be correlated with the high expression of the host-derived antimicrobial peptide aurelin. Furthermore, we recovered 43 high-quality metagenome-assembled genomes and determined the nutritional potential of the dominant Vibrio members. Interestingly, we observed increased abundances of genes related to the biosynthesis of amino acids, vitamins, and cofactors, as well as carbon fixation during the loss of host feeding ability, indicating the functional potential of Aurelia-associated microbiota to support the synthesis of essential nutrients. We also identified several potential mechanisms by which jellyfish-associated microbes establish stage-specific community structures and maintain stable colonization in dynamic host environments, including eukaryotic-like protein production, bacterial secretion systems, restriction-modification systems, and clustered regularly interspaced short palindromic repeats-Cas systems. Our study characterizes unique taxonomic and functional changes in jellyfish microbiomes during strobilation and provides foundations for uncovering the ancestral mechanism of host-microbe interactions during metamorphosis.
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Project description:The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.
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Project description:BackgroundThe correlation between the physical performance of athletes and their gut microbiota has become of growing interest in the past years, since new evidences have emerged regarding the importance of the gut microbiota as a main driver of the health status of athletes. In addition, it has been postulated that the metabolic activity of the microbial population harbored by the large intestine of athletes might influence their physical performances. Here, we analyzed 418 publicly available shotgun metagenomics datasets obtained from fecal samples of healthy athletes and healthy sedentary adults.ResultsThis study evidenced how agonistic physical activity and related lifestyle can be associated with the modulation of the gut microbiota composition, inducing modifications of the taxonomic profiles with an enhancement of gut microbes able to produce short-fatty acid (SCFAs). In addition, our analyses revealed a correlation between specific bacterial species and high impact biological synthases (HIBSs) responsible for the generation of a range of microbially driven compounds such vitamin B12, amino acidic derivatives, and other molecules linked to cardiovascular and age-related health-risk reduction.ConclusionsNotably, our findings show how subsist an association between competitive athletes, and modulation of the gut microbiota, and how this modulation is reflected in the potential production of microbial metabolites that can lead to beneficial effects on human physical performance and health conditions. Video Abstract.
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Project description:Soil salinization is spread in the dryland of NW China due to the dry or extreme dry climate. Increased salinization damages the health and function of soil systems and influences the microbial community structure and function. Some studies have been conducted to reveal the microbial community structure and isolate the microorganisms of saline soil or salt-lake sediments in this region. However, the functions of microorganisms and their response to salinization, i.e., their adaptation strategy to a wide salinization range in arid environments, are less understood. Here, we applied metagenomics technology to investigate the microbial community structure, function, and their relationship with salinization, and discussed the adaptative strategy of microorganisms to different saline environments. A total of 42 samples were sequenced on the Illumina PE500 platform. The archaea and bacteria constituted the dominant kingdoms; Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant bacterial phyla; and Euryarchaeota were the dominant archaeal phylum. The microbial communities showed significant structure divergence according to the salt concentration (saline (mean EC 22 mS/cm) and hypersaline (mean EC 70 mS/cm)), wherein the communities were dominated by bacteria in saline soils and archaea in hypersaline soils. Most of the dominant bacterial representation decreased with salinity, while the archaea increased with salinity. KEGG functional annotation showed that at level 2, the cell motility, environmental adaptation, signal transduction, signaling molecules and interaction, glycan biosynthesis and metabolism, and metabolism of other amino acids were reduced from saline to hypersaline, whereas the metabolism of cofactors and vitamins, folding sorting and degradation, replication and repair, transcription and translation, amino acid biosynthesis, glycolysis/gluconeogenesis, and carbon fixation increased with salinity. The increased salt content decreased the carbohydrate activities of microorganisms. The osmolyte regulation substance synthesis and absorption-related genes were more abundant in saline soils than in hypersaline soils, whereas the Na+/H+ antiporter genes (mnhB-E) and H+/Na+-transporting ATPase genes (atpA-F, I, K) were significantly higher in hypersaline soils. This indicated that in saline soils, microorganisms primarily synthesize and/or uptake compatible solutes to cope with osmotic stress, whereas in the hypersaline habitat, the high-salt-in strategy was predicated to be adopted by the halophilic/extremely halophilic microorganisms, coupled with a high abundance of replication and repair, cofactors and vitamin metabolism, nucleotide metabolism, and carbon fixation to provide energy and ensure cell regeneration. In conclusion, increases in salinity influence the microbial communities' structure and function, as well as the adaptation of microorganisms.
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Project description:Emerging evidence indicates maternal microbiota as one major reservoir for pioneering microbes in infants. However, the global distinct and identical features of mother-infant gut microbiota at various taxonomic resolutions and metabolic functions across cohorts and potential of infant microbial prediction based on their paired mother's gut microbiota remain unclear. Here, we analyzed 376 mother-infant dyads (468 mother and 1024 infant samples) of eight studies from six countries and observed higher diversity at species and strain levels in maternal gut microbiota but not their metabolic functions. A number of 290 species were shared in at least one mother-infant dyad, with 26 species (five at strain level) observed across cohorts. The profile of mother-infant shared species and strains was further influenced by delivery mode and feeding regimen. The mother-sourced species in infants exhibited similar strain heterogeneity but more metabolic functions compared to other-sourced species, suggesting the comparable stability and fitness of shared and non-shared species and the potential role of shared species in the early gut microbial community, respectively. Predictive models showed moderate performance accuracy for shared species and strains occurrences in infants. These generalized mother-infant shared species and strains may be considered as the primary targets for future work toward infant microbiome development and probiotics exploration.
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Project description:Metagenomic survey of the gut microbiome of term infants in the United States reveals widespread dysbiosis, absence of B. infantis, and high abundance of antibiotic resistance genes.
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