{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T17:30:40Z","timestamp":1787160640976,"version":"build-2736575974"},"reference-count":47,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T00:00:00Z","timestamp":1624924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nutrients"],"abstract":"<jats:p>The intestinal microbiome may trigger celiac disease (CD) in individuals with a genetic disposition when exposed to dietary gluten. Research demonstrates that nutrition during infancy is crucial to the intestinal microbiome engraftment. Very few studies to date have focused on the breast milk composition of subjects with a history of CD on a gluten-free diet. Here, we utilize a multi-omics approach with shotgun metagenomics to analyze the breast milk microbiome integrated with metabolome profiling of 36 subjects, 20 with CD on a gluten-free diet and 16 healthy controls. These analyses identified significant differences in bacterial and viral species\/strains and functional pathways but no difference in metabolite abundance. Specifically, three bacterial strains with increased abundance were identified in subjects with CD on a gluten-free diet of which one (Rothia mucilaginosa) has been previously linked to autoimmune conditions. We also identified five pathways with increased abundance in subjects with CD on a gluten-free diet. We additionally found four bacterial and two viral species\/strains with increased abundance in healthy controls. Overall, the differences observed in bacterial and viral species\/strains and in functional pathways observed in our analysis may influence microbiome engraftment in neonates, which may impact their future clinical outcomes.<\/jats:p>","DOI":"10.3390\/nu13072243","type":"journal-article","created":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T10:52:46Z","timestamp":1624963966000},"page":"2243","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet"],"prefix":"10.3390","volume":"13","author":[{"given":"Katherine L.","family":"Olshan","sequence":"first","affiliation":[{"name":"Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA"},{"name":"Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Boston, MA 02129, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02115, USA"},{"name":"Celiac Research Program, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali R.","family":"Zomorrodi","sequence":"additional","affiliation":[{"name":"Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA"},{"name":"Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Boston, MA 02129, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02115, USA"},{"name":"Celiac Research Program, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0313-3506","authenticated-orcid":false,"given":"Meritxell","family":"Pujolassos","sequence":"additional","affiliation":[{"name":"Theoreo srl, University of Salerno, 84084 Salerno, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2962-7379","authenticated-orcid":false,"given":"Jacopo","family":"Troisi","sequence":"additional","affiliation":[{"name":"Theoreo srl, University of Salerno, 84084 Salerno, Italy"},{"name":"Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Salerno, Italy"},{"name":"European Biomedical Research Institute of Salerno (EBRIS), Via S. De Renzi, 50, 84125 Salerno, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nayeim","family":"Khan","sequence":"additional","affiliation":[{"name":"CosmosID Inc., Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Fanelli","sequence":"additional","affiliation":[{"name":"CosmosID Inc., Rockville, MD 20850, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Kenyon","sequence":"additional","affiliation":[{"name":"Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Boston, MA 02129, USA"},{"name":"Celiac Research Program, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2134-0261","authenticated-orcid":false,"given":"Alessio","family":"Fasano","sequence":"additional","affiliation":[{"name":"Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA"},{"name":"Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Boston, MA 02129, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02115, USA"},{"name":"Celiac Research Program, Harvard Medical School, Boston, MA 02115, USA"},{"name":"Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Salerno, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maureen M.","family":"Leonard","sequence":"additional","affiliation":[{"name":"Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA"},{"name":"Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Boston, MA 02129, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02115, USA"},{"name":"Celiac Research Program, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,6,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1053\/gast.2000.8521","article-title":"Current concepts of celiac disease pathogenesis","volume":"119","author":"Schuppan","year":"2000","journal-title":"Gastroenterology"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.bpg.2015.04.004","article-title":"Genetics of celiac disease","volume":"29","author":"Wijmenga","year":"2015","journal-title":"Best Pract. Res. Clin. Gastroenterol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1056\/NEJMoa1400697","article-title":"Introduction of gluten, HLA status, and the risk of celiac disease in children","volume":"371","author":"Lionetti","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1056\/NEJMoa1404172","article-title":"Randomized feeding intervention in infants at high risk for celiac disease","volume":"371","author":"Vriezinga","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.trsl.2016.09.003","article-title":"Microbiome and food allergy","volume":"179","author":"Blazquez","year":"2017","journal-title":"Transl. Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1053\/j.gastro.2014.02.009","article-title":"The microbiome in inflammatory bowel disease: Current status and the future ahead","volume":"146","author":"Kostic","year":"2014","journal-title":"Gastroenterology"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1097\/MCG.0b013e31823711fd","article-title":"The Intestinal Microbiota and Obesity","volume":"46","author":"Kallus","year":"2012","journal-title":"J. Clin. Gastroenterol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1136\/adc.2005.082016","article-title":"Effect of breast feeding on risk of coeliac disease: A systematic review and meta-analysis of observational studies","volume":"91","author":"Akobeng","year":"2006","journal-title":"Arch. Dis. Child."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1111\/apt.12023","article-title":"Systematic review: Early infant feeding and the prevention of coeliac disease","volume":"36","author":"Szajewska","year":"2012","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"10410","DOI":"10.1038\/ncomms10410","article-title":"Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children","volume":"7","author":"Korpela","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.cell.2012.10.052","article-title":"Xenobiotics shape the physiology and gene expression of the active human gut microbiome","volume":"152","author":"Maurice","year":"2013","journal-title":"Cell"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1136\/gutjnl-2015-310861","article-title":"Proton pump inhibitors alter the composition of the gut microbiota","volume":"65","author":"Jackson","year":"2016","journal-title":"Gut"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1126\/science.1208344","article-title":"Linking long-term dietary patterns with gut microbial enterotypes","volume":"334","author":"Wu","year":"2011","journal-title":"Science"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1016\/j.chom.2015.04.004","article-title":"Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life","volume":"17","author":"Backhed","year":"2015","journal-title":"Cell Host. Microbe."},{"key":"ref_15","first-page":"61","article-title":"Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods","volume":"30","author":"Harmsen","year":"2000","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"De Palma, G., Capilla, A., Nova, E., Castillejo, G., Varea, V., Pozo, T., Garrote, J., Polanco, I., Lopez, A., and Ribes-Koninckx, C. (2012). Influence of milk-feeding type and genetic risk of developing coeliac disease on intestinal microbiota of infants: The PROFICEL study. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0030791"},{"key":"ref_17","first-page":"551","article-title":"Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: The PROFICEL study","volume":"9","author":"Olivares","year":"2018","journal-title":"Gut Microbes."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Leonard, M.K., Pujolassos, M., Troisi, J., Valitutti, F., Subramanian, P., Camhi, S., Kenyon, V., Colucci, A., Serena, G., and Cucchiara, S. (2020). Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease. Microbiome.","DOI":"10.21203\/rs.2.24237\/v2"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.phrs.2012.09.001","article-title":"The human milk microbiota: Origin and potential roles in health and disease","volume":"69","author":"Fernandez","year":"2013","journal-title":"Pharmacol. Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1128\/AEM.02063-08","article-title":"Isolation of bifidobacteria from breast milk and assessment of the bifidobacterial population by PCR-denaturing gradient gel electrophoresis and quantitative real-time PCR","volume":"75","author":"Martin","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1764","DOI":"10.1111\/j.1365-2222.2007.02849.x","article-title":"Maternal breast-milk and intestinal bifidobacteria guide the compositional development of the Bifidobacterium microbiota in infants at risk of allergic disease","volume":"37","author":"Gueimonde","year":"2007","journal-title":"Clin. Exp. Allergy"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1111\/j.1472-765X.2009.02567.x","article-title":"Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR","volume":"48","author":"Collado","year":"2009","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1046\/j.1365-2672.2003.02002.x","article-title":"Inhibition of Staphylococcus aureus by the commensal bacteria of human milk","volume":"95","author":"Heikkila","year":"2003","journal-title":"J. Appl. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1016\/j.jpeds.2003.09.028","article-title":"Human milk is a source of lactic acid bacteria for the infant gut","volume":"143","author":"Langa","year":"2003","journal-title":"J. Pediatr."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1177\/0890334404272393","article-title":"Probiotic potential of 3 Lactobacilli strains isolated from breast milk","volume":"21","author":"Olivares","year":"2005","journal-title":"J. Hum. Lact."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1007\/s00394-014-0692-1","article-title":"Human milk composition differs in healthy mothers and mothers with celiac disease","volume":"54","author":"Olivares","year":"2015","journal-title":"Eur. J. Nutr."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Ben\u00edtez-P\u00e1ez, A., Olivares, M., Szajewska, H., Pie\u015bcik-Lech, M., Polanco, I., Castillejo, G., Nu\u00f1ez, M., Ribes-Koninckx, C., Korponay-Szab\u00f3, I., and Koletzko, S. (2020). Breast-Milk Microbiota Linked to Celiac Disease Development in Children: A Pilot Study from the PreventCD Cohort. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01335"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"9325","DOI":"10.3390\/nu7115470","article-title":"Celiac Disease Genomic, Environmental, Microbiome, and Metabolomic (CDGEMM) Study Design: Approach to the Future of Personalized Prevention of Celiac Disease","volume":"7","author":"Leonard","year":"2015","journal-title":"Nutrients"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"45","DOI":"10.3389\/fnut.2019.00045","article-title":"What\u2019s Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study","volume":"6","author":"Lackey","year":"2019","journal-title":"Front. Nutr."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Aparicio, M., Alba, C., Proctocolitis Study Group Of Cam Public Health Area, Rodriguez, J.M., and Fernandez, L. (2020). Microbiological and Immunological Markers in Milk and Infant Feces for Common Gastrointestinal Disorders: A Pilot Study. Nutrients, 12.","DOI":"10.3390\/nu12030634"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Pace, R.M., Williams, J.E., Robertson, B., Lackey, K.A., Meehan, C.L., Price, W.J., Foster, J.A., Sellen, D.W., Kamau-Mbuthia, E.W., and Kamundia, E.W. (2021). Variation in Human Milk Composition Is Related to Differences in Milk and Infant Fecal Microbial Communities. Microorganisms, 9.","DOI":"10.3390\/microorganisms9061153"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Hasan, N.A.Y., Minard-Smith, A.T., Saeed, K., Li, H., Heizer, E.M., McMillan, N.J., Isom, R., Abdullah, A.S., Bornman, D.M., and Faith, S.A. (2014). Microbial community profiling of human saliva using shotgun metagenomic sequencing. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0097699"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1073\/pnas.1523817113","article-title":"Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed infection leading to necrotizing fasciitis","volume":"113","author":"Ponnusamy","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1038\/s41592-018-0176-y","article-title":"Species-level functional profiling of metagenomes and metatranscriptomes","volume":"15","author":"Franzosa","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_35","unstructured":"Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O\u2019Hara, R.B., Simpson, G.L., and Solymos, P. (2020, May 05). Vegan: Community Ecology Package, Available online: https:\/\/cran.r-project.org\/web\/packages\/vegan\/."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v022.i07","article-title":"The ecodist package for dissimilarity-based analysis of ecological data","volume":"22","author":"Goslee","year":"2007","journal-title":"J. Stat. Softw."},{"key":"ref_37","first-page":"50","article-title":"Infection with Rothia mucilaginosa: Review of Findings at a Danish Tertiary Hospital and Reports in Literature","volume":"15","author":"Spiegelhauer","year":"2019","journal-title":"EC Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2512","DOI":"10.3389\/fmicb.2018.02512","article-title":"Microbial Community Dynamics in Mother\u2019s Milk and Infant\u2019s Mouth and Gut in Moderately Preterm Infants","volume":"9","author":"Biagi","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1016\/j.jfda.2018.03.004","article-title":"Profiles of commensal and opportunistic bacteria in human milk from healthy donors in Taiwan","volume":"26","author":"Chen","year":"2018","journal-title":"J. Food Drug Anal."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Stinson, L.F., Sindi, A.S.M., Cheema, A.S., Lai, C.T., Muhlhausler, B.S., Wlodek, M.E., Payne, M.S., and Geddes, D.T. (2020). The human milk microbiome: Who, what, when, where, why, and how?. Nutr. Rev.","DOI":"10.1093\/nutrit\/nuaa029"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1017\/S0007114513000597","article-title":"Assessment of bacterial diversity in breast milk using culture-dependent and culture-independent approaches","volume":"110","author":"Jost","year":"2013","journal-title":"Br. J. Nutr."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.jinf.2020.01.023","article-title":"Breast milk microbiota: A review of the factors that influence composition","volume":"81","author":"Zimmermann","year":"2020","journal-title":"J. Infect."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1038\/s12276-020-0470-5","article-title":"Analysis of the human breast milk microbiome and bacterial extracellular vesicles in healthy mothers","volume":"52","author":"Kim","year":"2020","journal-title":"Exp. Mol. Med."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1039\/C8FO02182A","article-title":"Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China","volume":"10","author":"Ding","year":"2019","journal-title":"Food Funct."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"4548","DOI":"10.3748\/wjg.v23.i25.4548","article-title":"Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis","volume":"23","author":"Bajer","year":"2017","journal-title":"World J. Gastroenterol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1002\/ibd.20903","article-title":"Low counts of Faecalibacterium prausnitzii in colitis microbiota","volume":"15","author":"Sokol","year":"2009","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1186\/s40168-018-0611-4","article-title":"Signatures within the esophageal microbiome are associated with host genetics, age, and disease","volume":"6","author":"Deshpande","year":"2018","journal-title":"Microbiome"}],"container-title":["Nutrients"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6643\/13\/7\/2243\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:27:19Z","timestamp":1760164039000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6643\/13\/7\/2243"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,29]]},"references-count":47,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2021,7]]}},"alternative-id":["nu13072243"],"URL":"https:\/\/doi.org\/10.3390\/nu13072243","relation":{},"ISSN":["2072-6643"],"issn-type":[{"value":"2072-6643","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,29]]}}}