Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population

ABSTRACT A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosacchari...

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Autores principales:	Jan Majta, Krzysztof Odrzywolek, Bozena Milanovic, Vladyslav Hubar, Sonia Wrobel, Emilia Strycharz-Angrecka, Szymon Wojciechowski, Kaja Milanowska
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	bioinformatics gut microbiome infant microbiome machine learning microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ec6ad690c34d4db587bb79192ce23dea
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spelling	oai:doaj.org-article:ec6ad690c34d4db587bb79192ce23dea2021-11-15T15:22:22ZIdentification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population10.1128/mSphereDirect.00152-192379-5042https://doaj.org/article/ec6ad690c34d4db587bb79192ce23dea2019-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphereDirect.00152-19https://doaj.org/toc/2379-5042ABSTRACT A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides. IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout—the presented technology—utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.Jan MajtaKrzysztof OdrzywolekBozena MilanovicVladyslav HubarSonia WrobelEmilia Strycharz-AngreckaSzymon WojciechowskiKaja MilanowskaAmerican Society for Microbiologyarticlebioinformaticsgut microbiomeinfant microbiomemachine learningmicrobiomeMicrobiologyQR1-502ENmSphere, Vol 4, Iss 2 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	bioinformatics gut microbiome infant microbiome machine learning microbiome Microbiology QR1-502
spellingShingle	bioinformatics gut microbiome infant microbiome machine learning microbiome Microbiology QR1-502 Jan Majta Krzysztof Odrzywolek Bozena Milanovic Vladyslav Hubar Sonia Wrobel Emilia Strycharz-Angrecka Szymon Wojciechowski Kaja Milanowska Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population
description	ABSTRACT A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides. IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout—the presented technology—utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.
format	article
author	Jan Majta Krzysztof Odrzywolek Bozena Milanovic Vladyslav Hubar Sonia Wrobel Emilia Strycharz-Angrecka Szymon Wojciechowski Kaja Milanowska
author_facet	Jan Majta Krzysztof Odrzywolek Bozena Milanovic Vladyslav Hubar Sonia Wrobel Emilia Strycharz-Angrecka Szymon Wojciechowski Kaja Milanowska
author_sort	Jan Majta
title	Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population
title_short	Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population
title_full	Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population
title_fullStr	Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population
title_full_unstemmed	Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population
title_sort	identification of differentiating metabolic pathways between infant gut microbiome populations reveals depletion of function-level adaptation to human milk in the finnish population
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/ec6ad690c34d4db587bb79192ce23dea
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Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population

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