Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
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...
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Frontiers Media S.A.
2021-03-01
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Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2021.622550/full |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 Sophie E. Moore Andrew M. Prentice Debela Gindola K Gloria E. Otoo Rossina G. Pareja Lars Bode Mark A. McGuire Janet E. Williams Juan M. Rodríguez |
spellingShingle |
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 Sophie E. Moore Andrew M. Prentice Debela Gindola K Gloria E. Otoo Rossina G. Pareja Lars Bode Mark A. McGuire Janet E. Williams Juan M. Rodríguez Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome Frontiers in Cellular and Infection Microbiology human milk microbiota 16S rRNA bacteria sequencing reproducibility |
author_facet |
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 Sophie E. Moore Andrew M. Prentice Debela Gindola K Gloria E. Otoo Rossina G. Pareja Lars Bode Mark A. McGuire Janet E. Williams Juan M. Rodríguez |
author_sort |
Lorena Ruiz |
title |
Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome |
title_short |
Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome |
title_full |
Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome |
title_fullStr |
Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome |
title_full_unstemmed |
Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome |
title_sort |
comparison of two approaches for the metataxonomic analysis of the human milk microbiome |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Cellular and Infection Microbiology |
issn |
2235-2988 |
publishDate |
2021-03-01 |
description |
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 Registrationwww.clinicaltrials.gov, identifier NCT02670278. |
topic |
human milk microbiota 16S rRNA bacteria sequencing reproducibility |
url |
https://www.frontiersin.org/articles/10.3389/fcimb.2021.622550/full |
work_keys_str_mv |
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doaj-d4e02e5fdc7a4457935b428b145367ce2021-03-25T06:24:38ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882021-03-011110.3389/fcimb.2021.622550622550Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk MicrobiomeLorena Ruiz0Claudio Alba1Cristina García-Carral2Esther A. Jiménez3Kimberly A. Lackey4Michelle K. McGuire5Courtney L. Meehan6James Foster7Daniel W. Sellen8Elizabeth W. Kamau-Mbuthia9Egidioh W. Kamundia10Samwel Mbugua11Sophie E. Moore12Sophie E. Moore13Andrew M. Prentice14Debela Gindola K15Gloria E. Otoo16Rossina G. Pareja17Lars Bode18Mark A. McGuire19Janet E. Williams20Juan M. Rodríguez21Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, SpainDepartment of Nutrition and Food Science, Complutense University of Madrid, Madrid, SpainDepartment of Nutrition and Food Science, Complutense University of Madrid, Madrid, SpainDepartment of Nutrition and Food Science, Complutense University of Madrid, Madrid, SpainMargaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United StatesMargaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United StatesDepartment of Anthropology, Washington State University, Pullman, WA, United StatesMargaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United StatesDalla Lana School of Public Health, University of Toronto, Toronto, ON, CanadaDepartment of Human Nutrition, Egerton University, Nakuru, KenyaDepartment of Human Nutrition, Egerton University, Nakuru, KenyaDepartment of Human Nutrition, Egerton University, Nakuru, KenyaDivision of Women’s Health, King’s College London, London, United KingdomMRC Unit, Serekunda, GambiaMRC International Nutrition Group, London School of Hygiene and Tropical Medicine, London, United KingdomDepartment of Anthropology, Hawassa University, Hawassa, Ethiopia0Department of Nutrition and Food Science, University of Ghana, Accra, Ghana1Instituto de Investigación Nutricional, Lima, Peru2Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CoRE), University of California, San Diego, La Jolla, CA, United States3Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, United States3Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, United StatesDepartment of Nutrition and Food Science, Complutense University of Madrid, Madrid, SpainRecent 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 Registrationwww.clinicaltrials.gov, identifier NCT02670278.https://www.frontiersin.org/articles/10.3389/fcimb.2021.622550/fullhuman milkmicrobiota16S rRNAbacteriasequencing reproducibility |