Kimberly A Lackey1, Janet E Williams2, William J Price3, Janae M Carrothers1, Sarah L Brooker4, Bahman Shafii3, Mark A McGuire2, Michelle K McGuire5. 1. School of Biological Sciences, Washington State University, Pullman, WA, United States. 2. Department and Animal and Veterinary Science, University of Idaho, Moscow, ID, United States. 3. Statistical Programs, University of Idaho, Moscow, ID, United States. 4. Department and Animal and Veterinary Science, University of Idaho, Moscow, ID, United States; Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, United States. 5. School of Biological Sciences, Washington State University, Pullman, WA, United States; Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States. Electronic address: smcguire@wsu.edu.
Abstract
BACKGROUND: Inhibiting changes to bacteria in human milk between sample collection and analysis is necessary for unbiased characterization of the milk microbiome. Although cold storage is considered optimal, alternative preservation is sometimes necessary. RESEARCH AIM/QUESTION: The objective of this study was to compare the effectiveness of several commercially-available preservatives with regard to maintaining bacterial DNA in human milk for delayed microbiome analysis. Specifically, we compared Life Technologies' RNAlater® stabilization solution, Biomatrica's DNAgard® Saliva, Advanced Instruments' Broad Spectrum Microtabs II™, and Norgen Biotek Corporation's Milk DNA Preservation and Isolation Kit. METHODS: Aliquots of 8 pools of human milk were treated with each preservative. DNA was extracted immediately and at 1, 2, 4, and 6wk, during which time milk was held at 37°C. The V1-V3 region of the bacterial 16S rRNA gene was amplified and sequenced. Changes in bacterial community structure and diversity over time were evaluated. RESULTS: Comparable to other studies, the most abundant genera were Streptococcus (33.3%), Staphylococcus (14.0%), Dyella (6.3%), Pseudomonas (3.0%), Veillonella (2.5%), Hafnia (2.0%), Prevotella (1.7%), Rhodococcus (1.6%), and Granulicatella (1.4%). Overall, use of Norgen's Milk DNA Preservation and Isolation Kit best maintained the consistency of the bacterial community structure. Total DNA, diversity, and evenness metrics were also highest in samples preserved with this method. CONCLUSIONS: When collecting human milk for bacterial community analysis in field conditions where cold storage is not available, our results suggest that Norgen's Milk DNA Preservation and Isolation Kit may be a useful method, at least for a period of 2weeks.
BACKGROUND: Inhibiting changes to bacteria in human milk between sample collection and analysis is necessary for unbiased characterization of the milk microbiome. Although cold storage is considered optimal, alternative preservation is sometimes necessary. RESEARCH AIM/QUESTION: The objective of this study was to compare the effectiveness of several commercially-available preservatives with regard to maintaining bacterial DNA in human milk for delayed microbiome analysis. Specifically, we compared Life Technologies' RNAlater® stabilization solution, Biomatrica's DNAgard® Saliva, Advanced Instruments' Broad Spectrum Microtabs II™, and Norgen Biotek Corporation's Milk DNA Preservation and Isolation Kit. METHODS: Aliquots of 8 pools of human milk were treated with each preservative. DNA was extracted immediately and at 1, 2, 4, and 6wk, during which time milk was held at 37°C. The V1-V3 region of the bacterial 16S rRNA gene was amplified and sequenced. Changes in bacterial community structure and diversity over time were evaluated. RESULTS: Comparable to other studies, the most abundant genera were Streptococcus (33.3%), Staphylococcus (14.0%), Dyella (6.3%), Pseudomonas (3.0%), Veillonella (2.5%), Hafnia (2.0%), Prevotella (1.7%), Rhodococcus (1.6%), and Granulicatella (1.4%). Overall, use of Norgen's Milk DNA Preservation and Isolation Kit best maintained the consistency of the bacterial community structure. Total DNA, diversity, and evenness metrics were also highest in samples preserved with this method. CONCLUSIONS: When collecting human milk for bacterial community analysis in field conditions where cold storage is not available, our results suggest that Norgen's Milk DNA Preservation and Isolation Kit may be a useful method, at least for a period of 2weeks.
Authors: Katriona E Lyons; Fiona Fouhy; Carol-Anne O' Shea; C Anthony Ryan; Eugene M Dempsey; R Paul Ross; Catherine Stanton Journal: Microbiologyopen Date: 2020-12-29 Impact factor: 3.904
Authors: Michelle K McGuire; Arlo Z Randall; Antti E Seppo; Kirsi M Järvinen; Courtney L Meehan; Debela Gindola; Janet E Williams; Daniel W Sellen; Elizabeth W Kamau-Mbuthia; Egidioh W Kamundia; Samwel Mbugua; Sophie E Moore; Andrew M Prentice; James A Foster; Gloria E Otoo; Juan M Rodríguez; Rossina G Pareja; Lars Bode; Mark A McGuire; Joseph J Campo Journal: Front Immunol Date: 2021-02-11 Impact factor: 7.561
Authors: 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; Juan M Rodríguez Journal: Front Cell Infect Microbiol Date: 2021-03-25 Impact factor: 5.293
Authors: Kimberly A Lackey; Janet E Williams; Courtney L Meehan; Jessica A Zachek; Elizabeth D Benda; William J Price; James A Foster; Daniel W Sellen; Elizabeth W Kamau-Mbuthia; Egidioh W Kamundia; Samwel Mbugua; Sophie E Moore; Andrew M Prentice; Debela Gindola K; Linda J Kvist; Gloria E Otoo; Cristina García-Carral; Esther Jiménez; Lorena Ruiz; Juan M Rodríguez; Rossina G Pareja; Lars Bode; Mark A McGuire; Michelle K McGuire Journal: Front Nutr Date: 2019-04-17