Victora CG, Bahl R, Barros AJD, França GVA, Horton S, Krasevec J, et al. Breastfeeding in the 21st century: epidemiology, mechanisms, and lifelong effect. Lancet. 2016;387(10017):475–90.
Article
Google Scholar
Bode L. Human milk oligosaccharides: every baby needs a sugar mama. Glycobiology. 2012;22(9):1147–62.
Article
CAS
Google Scholar
Riskin A, Almog M, Peri R, Halasz K, Srugo I, Kessel A. Changes in immunomodulatory constituents of human milk in response to active infection in the nursing infant. Pediatr Res. 2012;71(2):220–5.
Article
CAS
Google Scholar
Wagner CL, Taylor SN, Johnson D. Host factors in amniotic fluid and breast milk that contribute to gut maturation. Clin Rev Allergy Immunol. 2008;34(2):191–204.
Article
Google Scholar
Sabbaj S, Ibegbu CC, Kourtis AP. Cellular immunity in breast milk: implications for postnatal transmission of HIV-1 to the infant. Adv Exp Med Biol. 2012;743:161–9.
Article
Google Scholar
Arrieta M-C, Stiemsma LT, Amenyogbe N, Brown EM, Finlay B. The intestinal microbiome in early life: health and disease. Front Immunol. 2014;5:427.
Article
Google Scholar
Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Chari RS, et al. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ. 2013;185(5):385–94.
Article
Google Scholar
Boix-Amorós A, Collado MC, Mira A. Relationship between milk microbiota, bacterial load, macronutrients, and human cells during lactation. Front Microbiol. 2016;7:492.
Fernández L, Langa S, Martín V, Maldonado A, Jiménez E, Martín R, et al. The human milk microbiota: origin and potential roles in health and disease. Pharmacol Res. 2013;69(1):1–10.
Article
Google Scholar
Jost T, Lacroix C, Braegger CP, Rochat F, Chassard C. Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding. Environ Microbiol. 2014;16(9):2891–904.
Article
CAS
Google Scholar
Murphy K, Curley D, O’Callaghan TF, O’Shea C-A, Dempsey EM, O’Toole PW, et al. The composition of human milk and infant faecal microbiota over the first three months of life: a pilot study. Sci Rep. 2017;7:40597.
Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 2017;171(7):647–54.
Vallès Y, Artacho A, Pascual-García A, Ferrús ML, Gosalbes MJ, Abellán JJ, et al. Microbial succession in the gut: directional trends of taxonomic and functional change in a birth cohort of Spanish infants. PLoS Genet. 2014;10(6):e1004406.
Article
Google Scholar
Binns C, Lee M, Low WY. The long-term public health benefits of breastfeeding. Asia Pac J Public Health. 2016;28(1):7–14.
Article
Google Scholar
Dieterich CM, Felice JP, O’Sullivan E, Rasmussen KM. Breastfeeding and health outcomes for the mother-infant dyad. Pediatr Clin N Am. 2013;60(1):31–48.
Article
Google Scholar
WHO. Short-term effects of breastfeeding: a systematic review on the benefits of breastfeeding on diarrhoea and pneumonia mortality. 2019. https://www.who.int/maternal_child_adolescent/documents/breastfeeding_short_term_effects/en/. Accessed 22 January 2019.
WHO. Long-term effects of breastfeeding: a systematic review. 2019. https://www.who.int/maternal_child_adolescent/documents/breastfeeding_long_term_effects/en/. Accessed 22 January 2019.
Uwaezuoke SN, Eneh CI, Ndu IK. Relationship between exclusive breastfeeding and lower risk of childhood obesity: a narrative review of published evidence. Clin Med Insights Pediatr. 2017;11:1179556517690196.
Article
Google Scholar
Cabrera-Rubio R, Mira-Pascual L, Mira A, Collado MC. Impact of mode of delivery on the milk microbiota composition of healthy women. J Dev Orig Health Dis. 2016;7(1):54–60.
Article
CAS
Google Scholar
Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, Mira A. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am J Clin Nutr. 2012;96(3):544–51.
Article
CAS
Google Scholar
Kumar H, du Toit E, Kulkarni A, Aakko J, Linderborg KM, Zhang Y, et al. Distinct patterns in human milk microbiota and fatty acid profiles across specific geographic locations. Front Microbiol. 2016;7:1619.
Urbaniak C, Angelini M, Gloor GB, Reid G. Human milk microbiota profiles in relation to birthing method, gestation and infant gender. Microbiome. 2016;4:1.
Article
Google Scholar
Moossavi S, Sepehri S, Robertson B, Bode L, Goruk S, Field CJ, et al. Composition and variation of the human milk microbiota are influenced by maternal and early-life factors. Cell Host Microbe. 2019;25(2):324–35 e4.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2019. https://CRAN.R-project.org/package=vegan. Accessed 23 January 2019.
Najafi F, Hasani J, Izadi N, Hashemi-Nazari S-S, Namvar Z, Mohammadi S, et al. The effect of prepregnancy body mass index on the risk of gestational diabetes mellitus: a systematic review and dose-response meta-analysis. Obes Rev. 2019;20(3):472–86.
Article
Google Scholar
Sze MA, Schloss PD. Looking for a signal in the noise: revisiting obesity and the microbiome. mBio. 2016;7(4):e01018–6.
Rodríguez JM. The origin of human milk bacteria: is there a bacterial entero-mammary pathway during late pregnancy and lactation? Adv Nutr. 2014;5(6):779–84.
Jeurink PV, van Bergenhenegouwen J, Jiménez E, Knippels LMJ, Fernández L, Garssen J, et al. Human milk: a source of more life than we imagine. Benef Microbes. 2013;4(1):17–30.
Article
CAS
Google Scholar
Biagi E, Quercia S, Aceti A, Beghetti I, Rampelli S, Turroni S, et al. The bacterial ecosystem of human milk and Infant’s mouth and gut. Front Microbiol. 2017;8:1214.
Article
Google Scholar
Gupta VK, Paul S, Dutta C. Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol. 2017;8:1162.
Drago L, Toscano M, De Grandi R, Grossi E, Padovani EM, Peroni DG. Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi. ISME J. 2017;11(4):875–84.
Article
CAS
Google Scholar
Lackey KA, Williams JE, Meehan CL, Zachek JA, Benda ED, Price WJ, et al. What’s normal? Microbiomes in human milk and infant feces are related to each other but vary geographically: The INSPIRE Study. Front Nutr. 2019;6:45.
Huttenhower C, Gevers D, Knight R, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.
Wang S, Li N, Zou H, Wu M. Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson’s disease. Neurosci Lett. 2019;696:93–8.
Osbourn A. Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation. Trends Genet. 2010;26(10):449–57.
Article
CAS
Google Scholar
O’Brien J, Wright GD. An ecological perspective of microbial secondary metabolism. Curr Opin Biotechnol. 2011;22(4):552–8.
Article
Google Scholar
Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, et al. Establishing microbial composition measurement standards with reference frames. Nat Commun. 2019;10(1):2719.
Article
Google Scholar
Stämmler F, Gläsner J, Hiergeist A, Holler E, Weber D, Oefner PJ, et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome. 2016;4(1):28.
Article
Google Scholar
Jian C, Luukkonen P, Yki-Järvinen H, Salonen A, Korpela K. Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling. PLoS One. 2020;15(1):e0227285.
Article
CAS
Google Scholar
Ley SH, O’Connor DL, Retnakaran R, Hamilton JK, Sermer M, Zinman B, et al. Impact of maternal metabolic abnormalities in pregnancy on human milk and subsequent infant metabolic development: methodology and design. BMC Public Health. 2010;10:590.
Article
Google Scholar
Ley SH, Hanley AJ, Sermer M, Zinman B, O’Connor DL. Associations of prenatal metabolic abnormalities with insulin and adiponectin concentrations in human milk. Am J Clin Nutr. 2012;95(4):867–74.
Article
CAS
Google Scholar
LeMay-Nedjelski L, Copeland J, Wang PW, Butcher J, Unger S, Stintzi A, et al. Methods and strategies to examine the human breastmilk microbiome. Methods Mol Biol. 1849;2018:63–86.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6(8):1621–4.
Article
CAS
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinforma Oxf Engl. 2010;26(19):2460–1.
Article
CAS
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–7.
Article
CAS
Google Scholar
Price LB, Liu CM, Melendez JH, Frankel YM, Engelthaler D, Aziz M, et al. Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota. PLoS One. 2009;4(7):e6462.
McMurdie PJ, Holmes S. Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data. Pac Symp Biocomput. 2012:235–46.
Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, et al. Piphillin: improved prediction of metagenomic content by direct inference from human microbiomes. PLoS One. 2016;11(11):e0166104.
Article
Google Scholar