Moossavi S, Miliku K, Sepehri S, Khafipour E, Azad MB. The prebiotic and probiotic properties of human milk: Implications for infant immune development and pediatric asthma. Front Pediatr. 2018;6:197. https://doi.org/10.3389/fped.2018.00197.

Article  PubMed  PubMed Central  Google Scholar 

Asnicar, F.; Manara, S.; Zolfo, M.; Truong, D.T.; Scholz, M.; Armanini, F.; et al. Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling. mSystems 2017; 2:e00164–16. https://doi.org/10.1128/mSystems.00164-16.

Biagi E, Quercia S, Aceti A, Beghetti I, Rampelli S, Turroni S, et al. The bacterial ecosystem of mother’s milk and infant’s mouth and gut. Front Microbiol. 2017;8:1214. https://doi.org/10.3389/fmicb.2017.01214.

Article  PubMed  PubMed Central  Google Scholar 

Biesbroek G, Bosch AATM, Wang X, Keijser BJF, Veenhoven RH, Sanders EAM, et al. The impact of breastfeeding on nasopharyngeal microbial communities in infants. Am J Respir Crit Care Med. 2014;190:298–308. https://doi.org/10.1164/rccm.201401-0073OC.

Article  PubMed  Google Scholar 

Ward TL, Hosid S, Ioshikhes I, Altosaar I. Human milk metagenome: A functional capacity analysis. BMC Microbiol. 2013;13:116. https://doi.org/10.1186/1471-2180-13-116.

Article  PubMed  PubMed Central  Google Scholar 

Li R, Tun HM, Jahan M, Zhang Z, Kumar A, Dilantha Fernando WG, et al. Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water. Sci Rep. 2017;7:5752. https://doi.org/10.1038/s41598-017-02516-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, et al. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome. 2021;9:17. https://doi.org/10.1186/s40168-020-00961-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nocker, A.; Cheung, C.-Y.; Camper, A.K. Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J Microbiol Methods 2006; 67:310–320. https://doi.org/10.1016/j.mimet.2006.04.015.

Turunen J, Tejesvi MV, Paalanne N, Hekkala J, Lindgren O, Kaakinen M, et al. Presence of distinctive microbiome in the first-pass meconium of newborn infants. Sci Rep. 2021;11:19449. https://doi.org/10.1038/s41598-021-98951-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong L, Liu H, Meng L, Xing M, Wang J, Wang C, et al. Quantitative PCR coupled with sodium dodecyl sulfate and propidium monoazide for detection of viable Staphylococcus aureus in milk. J Dairy Sci. 2018;101:4936–43. https://doi.org/10.3168/jds.2017-14087.

Article  CAS  PubMed  Google Scholar 

Miotto M, Barretta C, Ossai SO, da Silva HS, Kist A, Vieira CRW, et al. Optimization of a propidium monoazide-qPCR method for Escherichia coli quantification in raw seafood. Int J Food Microbiol. 2020;318: 108467. https://doi.org/10.1016/j.ijfoodmicro.2019.108467.

Article  CAS  PubMed  Google Scholar 

Stinson LF, Trevenen ML, Geddes DT. The viable microbiome of human milk differs from the metataxonomic profile. Nutrients. 2021;13:4445. https://doi.org/10.3390/nu13124445.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schwab C, Voney E, Ramirez Garcia A, Vischer M, Lacroix C. Characterization of the cultivable microbiota in fresh and stored mature human breast milk. Front Microbiol. 2019;10:2666. https://doi.org/10.3389/fmicb.2019.02666.

Article  PubMed  PubMed Central  Google Scholar 

Stinson LF, Trevenen ML, Geddes DT. Effect of cold storage on the viable and total bacterial populations in human milk. Nutrients. 2022;14:1875. https://doi.org/10.3390/nu14091875.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peters MDJ, McArthur A, Munn Z. Safe management of expressed breast milk: A systematic review. Women Birth. 2016;29:473–81. https://doi.org/10.1016/j.wombi.2016.05.007.

Article  PubMed  Google Scholar 

Becker, G.E.; Smith, H.A.; Cooney, F. Methods of milk expression for lactating women. Cochrane Database Syst Rev 2016; 9:CD006170. https://doi.org/10.1002/14651858.CD006170.pub5.

Kotásková I, Syrovátka V, Obručová H, Vídeňská P, Zwinsová B, Holá V, et al. Actinotignum schaalii: Relation to concomitants and connection to patients’ conditions in polymicrobial biofilms of urinary tract catheters and urines. Microorganisms. 2021;9:669. https://doi.org/10.3390/microorganisms9030669.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011;108:4516–22. https://doi.org/10.1073/pnas.1000080107.

Article  PubMed  Google Scholar 

Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (gene) amplicon sequencing pipeline. Front Microbiol. 2020;11: 550420. https://doi.org/10.3389/fmicb.2020.550420.

Article  PubMed  PubMed Central  Google Scholar 

Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, et al. Bioconda: Sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018;15:475–6. https://doi.org/10.1038/s41592-018-0046-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, et al. BioContainers: An open-source and community-driven framework for software standardization. Bioinformatics. 2017;33:2580–2. https://doi.org/10.1093/bioinformatics/btx192.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Babraham Bioinformatics. FastQC: A quality control tool for high throughput sequence data. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ [Accessed 9 Apr 2024].

Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047–8. https://doi.org/10.1093/bioinformatics/btw354.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3. https://doi.org/10.1038/nmeth.3869.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6. https://doi.org/10.1093/nar/gks1219.

Article  CAS  PubMed  Google Scholar 

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7. https://doi.org/10.1038/s41587-019-0209-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

R Core Team. R: A language and environment for statistical computing. Available from: https://www.r-project.org/ [Accessed 7 Sep 2024].

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin P, O’Hara B, et al. vegan: Community ecology package. R package version. 2015;2:2–1.

Google Scholar 

Gloor GB, Macklaim JM, Fernandes AD. Displaying variation in large datasets: A visual summary of effect sizes. J Comput Graph Stat. 2016. https://doi.org/10.1080/10618600.2015.1131161.

Article  Google Scholar 

Paradis E, Schliep K. ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 2019;35:526–8.

Article  CAS  PubMed  Google Scholar 

Wickham, H. ggplot2: Elegant graphics for data analysis. Springer; 2016. ISBN 978–3–319–24275–0.

Ahlmann-Eltze, C.; Patil, I. ggsignif: R package for displaying significance brackets for ggplot2. 2021.

Patil I. Visualizations with statistical details: The ggstatsplot approach. J Open Source Softw. 2021;6:3167. https://doi.org/10.21105/joss.03167.

Article