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Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome

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Lorena Ruiz, Claudio Alba, Cristina García-Carral, Esther A. Jiménez, Kimberly A. Lackey, Michelle K. McGuire, Courtney L. Meehan, James Foster, Daniel W. Sellen, Elizabeth W. Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Gloria E. Otoo, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Janet E. Williams & 1 more Juan M. Rodríguez

Original languageEnglish
Article number622550
JournalFrontiers in Cellular and Infection Microbiology
Volume11
DOIs
Published25 Mar 2021

Bibliographical note

Funding Information: We sincerely thank Andrew Doel (Medical Research Council Unit, The Gambia) for logistics planning and field supervision and Alansan Sey for questionnaire administration and taking anthropometric measurements in The Gambia; Jane Odei (University of Ghana) for supervising data collection in Ghana; DG (Hawassa University), Dubale Gebeyehu (Hawassa University), Haile Belachew (Hawassa University), and Birhanu Sintayehu for planning, logistics, recruiting, and data collection and the administration and staff at Adare Hospital in Hawassa for assistance with logistics in Ethiopia; Catherine O Sarange (Egerton University) for field supervision and logistics planning and Milka W. Churuge and Minne M. Gachau for recruiting, questionnaire administration, and taking anthropometric measurements in Kenya; Gisella Barbagelatta (Instituto de Investigaci?n Nutricional) for field supervision and logistics planning, Patricia Calderon (Instituto de Investigaci?n Nutricional) for recruiting, questionnaire administration, and taking anthropometric measurements, and Roxana Barrutia (Instituto de Investigaci?n Nutricional) for the management and shipping of samples in Peru; Le?nides Fern?ndez and Irene Espinosa Martos (Complutense University of Madrid) for technical assistance, expertise, and review of the manuscript and M. ?ngeles Checa (Zaragoza, Spain), Katalina Legarra (Guernica, Spain), and Julia M?nguez (Huesca, Spain) for participation in the collection of samples in Spain; Kirsti Kaski and Maije Sj?strand (both Helsingborg Hospital) for participation in the collection of samples, questionnaire administration, and anthropometric measurements in Sweden; Renee Bridge and Kara Sunderland (both from University of California, San Diego, CA, USA) and Janae Carrothers (Washington State University) for logistics planning, recruiting, questionnaire administration, sample collection, and taking anthropometric measurements in California and Washington; and Glenn Miller (Washington State University) for his expertise and critical logistic help that were needed for shipping samples and supplies worldwide. Publisher Copyright: © Copyright © 2021 Ruiz, Alba, García-Carral, Jiménez, Lackey, McGuire, Meehan, Foster, Sellen, Kamau-Mbuthia, Kamundia, Mbugua, Moore, Prentice, Gindola K, Otoo, Pareja, Bode, McGuire, Williams and Rodríguez. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

King's Authors

Abstract

Recent work has demonstrated the existence of large inter-individual and inter-population variability in the microbiota of human milk from healthy women living across variable geographical and socio-cultural settings. However, no studies have evaluated the impact that variable sequencing approaches targeting different 16S rRNA variable regions may have on the human milk microbiota profiling results. This hampers our ability to make meaningful comparisons across studies. In this context, the main purpose of the present study was to re-process and re-sequence the microbiome in a large set of human milk samples (n = 412) collected from healthy women living at diverse international sites (Spain, Sweden, Peru, United States, Ethiopia, Gambia, Ghana and Kenya), by targeting a different 16S rRNA variable region and reaching a larger sequencing depth. Despite some differences between the results obtained from both sequencing approaches were notable (especially regarding alpha and beta diversities and Proteobacteria representation), results indicate that both sequencing approaches revealed a relatively consistent microbiota configurations in the studied cohorts. Our data expand upon the milk microbiota results we previously reported from the INSPIRE cohort and provide, for the first time across globally diverse populations, evidence of the impact that different DNA processing and sequencing approaches have on the microbiota profiles obtained for human milk samples. Overall, our results corroborate some similarities regarding the microbial communities previously reported for the INSPIRE cohort, but some differences were also detected. Understanding the impact of different sequencing approaches on human milk microbiota profiles is essential to enable meaningful comparisons across studies. Clinical Trial Registration: www.clinicaltrials.gov, identifier NCT02670278.

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