Maturational patterns of the infant gut mycobiome are associated with early-life body mass index

Gutierrez, Mackenzie W.; Mercer, Emily M.; Moossavi, Shirin; Laforest‐Lapointe, Isabelle; Reyna, Myrtha E.; Becker, Allan B.; Simons, Elinor; Mandhane, Piush J.; Turvey, Stuart E.; Moraes, Theo J.; Sears, Malcolm R.; Subbarao, Padmaja; Azad, Meghan B.; Arrieta, Marie‐Claire

doi:10.1016/j.xcrm.2023.100928

Cited by 10 publications

(10 citation statements)

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“…Thus, to differentiate M. restricta -induced immune responses from other immunogenic gut commensals, we upgraded the Oligo-MM12 consortium to also include C. albicans (isolate K3) and Pseudomonas fluorescens (isolate J4) (B+CP), isolated from ANTIBIO infant stool samples, and compared it to mice colonized with all species and M. restricta (B+CP+M). C. albicans is a common intestinal colonizer, identified in fecal samples from a very early age 74,75 , and induces strong mucosal immune responses 16,62,76 . P. fluorescens is a recently appreciated member of the intestinal microbiome, with strong immunogenic effects in mammals 77,78 .…”

Section: Resultsmentioning

confidence: 99%

“…In line with this, reduced birth weight and antibiotic treatment duration have been associated with Malassezia skin colonization, and lung and systemic infections in term and preterm infants [88][89][90][91] . Species of this genus, such as M. globosa, M. restricta, M. sympodialis, and M. furfur are common colonizers of the skin 92,93 but some are commonly found in the gut as well, particularly during infancy 8,75,94,95 . Patterns of mycobiome development during the first year of life reveal a higher predominance of Malassezia spp.…”

Section: Discussionmentioning

confidence: 99%

“…In-house extracted DNA samples were sent to Microbiome Insights (Vancouver, Canada) for ITS2 and 16S amplicon sequencing. The ITS2 and 16S V4 regions were amplified and sequenced as previously described 29,75,122 . Demultiplexed forward and reverse reads were denoised, filtered, inferenced, trimmed, and merged using DADA2 v.1.26.0 123 package for R (R Development Core Team; http://www.R-project.org).…”

Section: Methodsmentioning

confidence: 99%

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Antibiotic-inducedMalasseziaspp. expansion in infants promotes early-life immune dysregulation and airway inflammation in mice

Bernardes,

Gutierrez,

Nguyen

et al. 2024

Preprint

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Antibiotics have deleterious consequences for the gut microbiome and can increase the risk of childhood asthma. While the effects of antibiotics on the bacterial microbiome and asthma risk are well characterized, their impact on the fungal microbiome (mycobiome) remains vastly unexplored. We investigated the effect of antibiotic use on the gut mycobiome in an observational, prospective clinical study of young infants. Antibiotic treatment resulted in increased fungal abundance and expansion of the yeast Malassezia spp. Based on these findings, germ-free mouse pups were colonized with a defined consortium of mouse-derived bacteria (Oligo-MM12) with or without Malassezia restricta. Colonization with this yeast increased myeloid and lymphoid intestinal immune responses deemed critical in atopy development, and elevated airway inflammation in house-dust mite (HDM)-challenged mice. Further evaluation in eosinophil-deficient mice revealed that the observed immune response is partially dependent on this cell type. This translational work demonstrates that fungal overgrowth and expansion of Malassezia spp. are previously overlooked collateral effects of infant antibiotic use, which may offer a potential strategy to prevent or mitigate pediatric asthma and related conditions.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Antibiotic-inducedMalasseziaspp. expansion in infants promotes early-life immune dysregulation and airway inflammation in mice

Bernardes,

Gutierrez,

Nguyen

et al. 2024

Preprint

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“…Taxonomic assignment based on amplicon sequence variants (ASVs) was performed using the following databases at 99% sequence similarity: SILVA v.132 [ 47 ] for bacteria (16S) and UNITE v.8.0 [ 48 ] for fungi (ITS2). Pre-processing of bacterial and fungal data was performed using phyloseq v.1.42.0 [ 49 ] and has been previously reported [ 35 , 36 ]. In brief, 954 unique bacterial ASVs were identified.…”

Section: Methodsmentioning

confidence: 99%

“…In this work, we begin to address this knowledge gap by evaluating both bacterial and fungal gut microbiome maturation patterns in 100 infants from the CHILD Cohort Study [ 34 ] over the first year of life using individual-level and multi-kingdom perspectives. Using a similar approach for mycobiome maturation, we have previously shown increasing vs. decreasing fungal richness over the first year of life is differentially associated with early childhood body mass index (BMI) z-scores in this sub-cohort, with this relationship being mediated by the influence of antibiotics exposure, maternal BMI and diet, and bacterial beta diversity [ 35 ]. Here, we determined that divergent patterns of bacterial and fungal gut microbiome maturation are more common in term-born infants than previously considered, occurring in over 40% of infants in this sub-cohort, which are characterized by differences in ecological and metabolic properties that may reflect altered rates of microbiome maturation.…”

Section: Introductionmentioning

confidence: 99%

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition

Mercer,

Ramay,

Moossavi

et al. 2024

Microbiome

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Background The gut microbiome undergoes primary ecological succession over the course of early life before achieving ecosystem stability around 3 years of age. These maturational patterns have been well-characterized for bacteria, but limited descriptions exist for other microbiota members, such as fungi. Further, our current understanding of the prevalence of different patterns of bacterial and fungal microbiome maturation and how inter-kingdom dynamics influence early-life microbiome establishment is limited. Results We examined individual shifts in bacterial and fungal alpha diversity from 3 to 12 months of age in 100 infants from the CHILD Cohort Study. We identified divergent patterns of gut bacterial or fungal microbiome maturation in over 40% of infants, which were characterized by differences in community composition, inter-kingdom dynamics, and microbe-derived metabolites in urine, suggestive of alterations in the timing of ecosystem transitions. Known microbiome-modifying factors, such as formula feeding and delivery by C-section, were associated with atypical bacterial, but not fungal, microbiome maturation patterns. Instead, fungal microbiome maturation was influenced by prenatal exposure to artificially sweetened beverages and the bacterial microbiome, emphasizing the importance of inter-kingdom dynamics in early-life colonization patterns. Conclusions These findings highlight the ecological and environmental factors underlying atypical patterns of microbiome maturation in infants, and the need to incorporate multi-kingdom and individual-level perspectives in microbiome research to improve our understandings of gut microbiome maturation patterns in early life and how they relate to host health.

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Cross‐Sectional and Prospective Association of Serum 25‐Hydroxyvitamin D with Gut Mycobiota during Pregnancy among Women with Gestational Diabetes

Liang,

Jiang,

et al. 2024

Molecular Nutrition Food Res

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ScopeLittle is known about the effect of blood vitamin D status on the gut mycobiota (i.e., fungi), a crucial component of the gut microbial ecosystem. The study aims to explore the association between 25‐hydroxyvitamin D [25(OH)D] and gut mycobiota and to investigate the link between the identified mycobial features and blood glycemic traits.Methods and resultsThe study examines the association between serum 25(OH)D levels and the gut mycobiota in the Westlake Precision Birth Cohort, which includes pregnant women with gestational diabetes mellitus (GDM). The study develops a genetic risk score (GRS) for 25(OH)D to validate the observational results. In both the prospective and cross‐sectional analyses, the vitamin D is associated with gut mycobiota diversity. Specifically, the abundance of Saccharomyces is significantly lower in the vitamin D‐sufficient group than in the vitamin D‐deficient group. The GRS of 25(OH)D is inversely associated with the abundance of Saccharomyces. Moreover, the Saccharomyces is positively associated with blood glucose levels.ConclusionBlood vitamin D status is associated with the diversity and composition of gut mycobiota in women with GDM, which may provide new insights into the mechanistic understanding of the relationship between vitamin D levels and metabolic health.

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Maturational patterns of the infant gut mycobiome are associated with early-life body mass index

Cited by 10 publications

References 98 publications

Antibiotic-inducedMalasseziaspp. expansion in infants promotes early-life immune dysregulation and airway inflammation in mice

Antibiotic-inducedMalasseziaspp. expansion in infants promotes early-life immune dysregulation and airway inflammation in mice

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition

Cross‐Sectional and Prospective Association of Serum 25‐Hydroxyvitamin D with Gut Mycobiota during Pregnancy among Women with Gestational Diabetes

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