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      What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study

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          Abstract

          Background: Microbial communities in human milk and those in feces from breastfed infants vary within and across populations. However, few researchers have conducted cross-cultural comparisons between populations, and little is known about whether certain “core” taxa occur normally within or between populations and whether variation in milk microbiome is related to variation in infant fecal microbiome. The purpose of this study was to describe microbiomes of milk produced by relatively healthy women living at diverse international sites and compare these to the fecal microbiomes of their relatively healthy infants.

          Methods: We analyzed milk ( n = 394) and infant feces ( n = 377) collected from mother/infant dyads living in 11 international sites (2 each in Ethiopia, The Gambia, and the US; 1 each in Ghana, Kenya, Peru, Spain, and Sweden). The V1-V3 region of the bacterial 16S rRNA gene was sequenced to characterize and compare microbial communities within and among cohorts.

          Results: Core genera in feces were Streptococcus, Escherichia/Shigella, and Veillonella, and in milk were Streptococcus and Staphylococcus, although substantial variability existed within and across cohorts. For instance, relative abundance of Lactobacillus was highest in feces from rural Ethiopia and The Gambia, and lowest in feces from Peru, Spain, Sweden, and the US; Rhizobium was relatively more abundant in milk produced by women in rural Ethiopia than all other cohorts. Bacterial diversity also varied among cohorts. For example, Shannon diversity was higher in feces from Kenya than Ghana and US-California, and higher in rural Ethiopian than Ghana, Peru, Spain, Sweden, and US-California. There were limited associations between individual genera in milk and feces, but community-level analyses suggest strong, positive associations between the complex communities in these sample types.

          Conclusions: Our data provide additional evidence of within- and among-population differences in milk and infant fecal bacterial community membership and diversity and support for a relationship between the bacterial communities in milk and those of the recipient infant's feces. Additional research is needed to understand environmental, behavioral, and genetic factors driving this variation and association, as well as its significance for acute and chronic maternal and infant health.

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          The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

          SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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                Author and article information

                Contributors
                Journal
                Front Nutr
                Front Nutr
                Front. Nutr.
                Frontiers in Nutrition
                Frontiers Media S.A.
                2296-861X
                17 April 2019
                2019
                : 6
                : 45
                Affiliations
                [1] 1Margaret Ritchie School of Family and Consumer Sciences, University of Idaho , Moscow, ID, United States
                [2] 2Department of Animal and Veterinary Science, University of Idaho , Moscow, ID, United States
                [3] 3Department of Anthropology, Washington State University , Pullman, WA, United States
                [4] 4Statistical Programs, College of Agricultural and Life Sciences, University of Idaho , Moscow, ID, United States
                [5] 5Department of Biological Sciences, University of Idaho , Moscow, ID, United States
                [6] 6Dalla Lana School of Public Health, University of Toronto , Toronto, ON, Canada
                [7] 7Department of Human Nutrition, Egerton University , Nakuru, Kenya
                [8] 8Department of Women and Children's Health, King's College London , London, United Kingdom
                [9] 9MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine , Fajara, Gambia
                [10] 10MRC International Nutrition Group, London School of Hygiene and Tropical Medicine , London, United Kingdom
                [11] 11Department of Anthropology, Hawassa University , Hawassa, Ethiopia
                [12] 12Faculty of Medicine, Lund University , Lund, Sweden
                [13] 13Department of Nutrition and Food Science, University of Ghana , Accra, Ghana
                [14] 14Probisearch , Tres Cantos, Spain
                [15] 15Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC) , Villaviciosa, Spain
                [16] 16Department of Nutrition, Food Science, and Food Technology, Complutense University of Madrid , Madrid, Spain
                [17] 17Nutrition Research Institute , Lima, Peru
                [18] 18Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California, San Diego , La Jolla, CA, United States
                [19] 19Department of Pediatrics, University of California, San Diego , La Jolla, CA, United States
                Author notes

                Edited by: Aldo Corsetti, University of Teramo, Italy

                Reviewed by: Arianna Aceti, University of Bologna, Italy; Veronique Demers-Mathieu, Oregon State University, United States

                *Correspondence: Michelle K. McGuire smcguire@ 123456uidaho.edu

                This article was submitted to Food Microbiology, a section of the journal Frontiers in Nutrition

                Article
                10.3389/fnut.2019.00045
                6479015
                31058158
                fcecaea7-80ba-4790-93cd-23ee878aca35
                Copyright © 2019 Lackey, Williams, Meehan, Zachek, Benda, Price, Foster, Sellen, Kamau-Mbuthia, Kamundia, Mbugua, Moore, Prentice, K., Kvist, Otoo, García-Carral, Jiménez, Ruiz, Rodríguez, Pareja, Bode, McGuire and McGuire.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 20 December 2018
                : 27 March 2019
                Page count
                Figures: 6, Tables: 5, Equations: 0, References: 70, Pages: 20, Words: 15843
                Funding
                Funded by: Ministerio de Economía y Competitividad 10.13039/501100003329
                Funded by: European Commission 10.13039/501100000780
                Funded by: National Institutes of Health 10.13039/100000002
                Funded by: Division of Integrative Organismal Systems 10.13039/100000154
                Categories
                Nutrition
                Original Research

                human milk,breastmilk,feces,microbiome,international,infant,breastfeeding,maternal

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