Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants.

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Abstract

Individuals with inactive alleles of the fucosyltransferase 2 gene (FUT2; termed the 'secretor' gene) are common in many populations. Some members of the genus Bifidobacterium, common infant gut commensals, are known to consume 2'-fucosylated glycans found in the breast milk of secretor mothers. We investigated the effects of maternal secretor status on the developing infant microbiota with a special emphasis on bifidobacterial species abundance.

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Most cited references 66

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

J. Gregory Caporaso, Christian L. Lauber, William A. Walters … (2011)

The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.

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Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

N Fierer, J W Leff, B. J. Adams … (2012)

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

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The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome.

D. A. Sela, J. Chapman, A Adeuya … (2008)

Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrient-utilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype.

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Author and article information

Journal

Journal ID (iso-abbrev): Microbiome

Title: Microbiome

Publisher: Springer Nature

ISSN: 2049-2618

ISSN (Print): 2049-2618

Publication date (Electronic): 2015

Volume: 3

Affiliations

[1 ] Department of Food Science and Technology, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA ; Foods For Health Institute, UC Davis, 1 Peter J Shields Avenue, Davis, CA 95616 USA.

[2 ] Department of Chemistry, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA ; Foods For Health Institute, UC Davis, 1 Peter J Shields Avenue, Davis, CA 95616 USA.

[3 ] Department of Life Sciences, PhD School in Science and Technologies for Health Products, University of Modena and Reggio Emilia, Via Università, 4, Modena, MO 41100 Italy.

[4 ] Department of Chemistry, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA.

[5 ] Genome Center, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA.

[6 ] Department of Food Science and Human Nutrition, University Illinois at Urbana-Champaign, S. Goodwin Ave., Urbana, IL 61801 USA.

[7 ] Department of Food Science and Technology, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA ; Department of Viticulture and Enology, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA ; Foods For Health Institute, UC Davis, 1 Peter J Shields Avenue, Davis, CA 95616 USA.

Article

Publisher Item ID: 71

DOI: 10.1186/s40168-015-0071-z

PMC ID: 4412032

PubMed ID: 25922665

SO-VID: b8141b90-226f-484d-a83d-0a37f5655d08

History

Keywords: Breastfeeding,Bifidobacteria,FUT2,Human milk oligosaccharides,Infant,Marker gene sequencing,Secretor,Short-chain fatty acids

Data availability:

Keywords: Breastfeeding, Bifidobacteria, FUT2, Human milk oligosaccharides, Infant, Marker gene sequencing, Secretor, Short-chain fatty acids

Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants.

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Abstract

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Most cited references 66

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome.

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