{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T02:25:55Z","timestamp":1787019955699,"version":"build-2736575974"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T00:00:00Z","timestamp":1721865600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T00:00:00Z","timestamp":1721865600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"DOI":"10.1186\/s12864-024-10618-2","type":"journal-article","created":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T01:25:16Z","timestamp":1721870716000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort"],"prefix":"10.1186","volume":"25","author":[{"given":"Taona Emmah","family":"Mudhluli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magdalena","family":"Kujawska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Mueller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela","family":"Felsl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bastian-Alexander","family":"Truppel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindsay J.","family":"Hall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inam","family":"Chitsike","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Exnevia","family":"Gomo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danai Tavonga","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,25]]},"reference":[{"key":"10618_CR1","first-page":"14","volume":"2023","author":"DT Zhou","year":"2023","unstructured":"Zhou DT, Mudhluli TE, Hall LJ, Manasa J, Munyati S. A Scoping review of early-life gut microbiota and Bifidobacterium research in Zimbabwe. Paediatr Health Med Ther. 2023;2023:14.","journal-title":"Paediatr Health Med Ther"},{"key":"10618_CR2","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1080\/01635581.2019.1602659","volume":"71","author":"L Katsidzira","year":"2019","unstructured":"Katsidzira L, Ocvirk S, Wilson A, et al. Differences in fecal gut microbiota, short-chain fatty acids and bile acids link colorectal cancer risk to dietary changes associated with urbanization among Zimbabweans. Nutr Cancer. 2019;71:8.","journal-title":"Nutr Cancer"},{"key":"10618_CR3","doi-asserted-by":"publisher","first-page":"103421","DOI":"10.1016\/j.ebiom.2021.103421","volume":"68","author":"EK Gough","year":"2021","unstructured":"Gough EK, Edens TJ, Geum HM, et al. For SHINE trial team, maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe. EBiomedicine J. 2021;68:103421.","journal-title":"EBiomedicine J"},{"issue":"4","key":"10618_CR4","doi-asserted-by":"publisher","first-page":"1104","DOI":"10.1080\/19490976.2020.1717299","volume":"11","author":"EK Gough","year":"2020","unstructured":"Gough EK, Bourke CD, Berejena C, et al. Strain-level analysis of gut-resident pro-inflammatory viridans group Streptococci suppressed by long-term cotrimoxazole prophylaxis among HIV-positive children in Zimbabwe. Gut Microbes. 2020;11(4):1104\u201315.","journal-title":"Gut Microbes"},{"key":"10618_CR5","doi-asserted-by":"publisher","first-page":"101368","DOI":"10.1016\/j.isci.2020.101368","volume":"23","author":"M Kujawska","year":"2020","unstructured":"Kujawska M, La Rosa SL, Roger LC, Pope PB, Hoyles L, McCartney AL, et al. Succession of Bifidobacterium longum strains in response to a changing early life nutritional environment reveals dietary substrate adaptations. iScience. 2020;23:101368.","journal-title":"iScience"},{"key":"10618_CR6","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/s41396-019-0553-2","volume":"14","author":"MAE Lawson","year":"2020","unstructured":"Lawson MAE, O\u2019Neill IJ, Kujawska M, Javvadi SG, Wijeyesekera A, Flegg Z, et al. Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. ISME J. 2020;14:635\u201348.","journal-title":"ISME J"},{"issue":"3","key":"10618_CR7","doi-asserted-by":"publisher","first-page":"e0265123","DOI":"10.1371\/journal.pone.0265123","volume":"17","author":"OT Oyedemi","year":"2022","unstructured":"Oyedemi OT, Shaw S, Martin JC, Ayeni FA, Scott KP. Changes in the gut microbiota of Nigerian infants within the first year of life. PLoS One. 2022;17(3):e0265123.","journal-title":"PLoS One"},{"issue":"5","key":"10618_CR8","doi-asserted-by":"publisher","first-page":"4745","DOI":"10.3390\/ijerph110504745","volume":"11","author":"S Fijan","year":"2014","unstructured":"Fijan S. Microorganisms with claimed probiotic properties: an overview of recent literature. Int J Environ Res Public Health. 2014;11(5):4745\u201367.","journal-title":"Int J Environ Res Public Health"},{"key":"10618_CR9","volume-title":"Health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria","author":"Food and Agricultural Organization of the United Nations and World Health Organization","year":"2002","unstructured":"Food and Agricultural Organization of the United Nations and World Health Organization. Health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria. World Health Organization; 2002."},{"issue":"7","key":"10618_CR10","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1016\/j.tim.2010.03.008","volume":"18","author":"DA Sela","year":"2010","unstructured":"Sela DA, Mills DA. Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides. Trends Microbiol. 2010;18(7):298\u2013307.","journal-title":"Trends Microbiol"},{"issue":"10","key":"10618_CR11","doi-asserted-by":"publisher","first-page":"2667","DOI":"10.1111\/j.1462-2920.2011.02533.x","volume":"13","author":"P Van den Abbeele","year":"2011","unstructured":"Van den Abbeele P, G\u00e9rard P, Rabot S, Bruneau A, El Aidy S, Derrien M, et al. Arabinoxylans and inulin differentially modulate the mucosal and luminal gut microbiota and mucin-degradation in humanized rats. Environ Microbiol. 2011;13(10):2667\u201380.","journal-title":"Environ Microbiol"},{"issue":"12","key":"10618_CR12","first-page":"4826","volume":"19","author":"S Duranti","year":"2017","unstructured":"Duranti S, Milani C, Lugli GA. Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum. Environ Microbiol. 2017;19(12):4826\u201338.","journal-title":"Environ Microbiol"},{"key":"10618_CR13","doi-asserted-by":"publisher","first-page":"202","DOI":"10.3389\/fmicb.2013.00202","volume":"4","author":"M Gueimonde","year":"2013","unstructured":"Gueimonde M, S\u00e1nchez B, Reyes-Gavil\u00e1n CG, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol. 2013;4:202.","journal-title":"Front Microbiol"},{"key":"10618_CR14","doi-asserted-by":"publisher","first-page":"3129439","DOI":"10.1155\/2022\/3129439","volume":"2022","author":"M Georges","year":"2022","unstructured":"Georges M, Odoyo E, Matano D, Tiria F, Kyany\u2019a C, Mbwika D, et al. Determination of Enterococcus faecalis and Enterococcus faecium antimicrobial resistance and virulence factors and their association with clinical and demographic factors in Kenya. J Pathog. 2022;2022:3129439.","journal-title":"J Pathog"},{"issue":"7","key":"10618_CR15","first-page":"535","volume":"13","author":"M Ventura","year":"2015","unstructured":"Ventura M, O\u2019Flaherty S, Claesson MJ. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Microbiol. 2015;13(7):535\u201346.","journal-title":"Nat Rev Microbiol"},{"issue":"8","key":"10618_CR16","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.3389\/fmicb.2017.01162","volume":"23","author":"VK Gupta","year":"2017","unstructured":"Gupta VK, Paul S, Dutta C. Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol. 2017;23(8):1162.","journal-title":"Front Microbiol."},{"issue":"14","key":"10618_CR17","doi-asserted-by":"publisher","first-page":"1823","DOI":"10.1093\/bioinformatics\/bts252","volume":"28","author":"E Pruesse","year":"2012","unstructured":"Pruesse E, Peplies J, Glockner FO. SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28(14):1823\u20139.","journal-title":"Bioinformatics"},{"issue":"17","key":"10618_CR18","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884\u201390.","journal-title":"Bioinformatics"},{"issue":"6","key":"10618_CR19","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","volume":"13","author":"RR Wick","year":"2017","unstructured":"Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595.","journal-title":"PLoS Comput Biol"},{"issue":"7","key":"10618_CR20","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043\u201355.","journal-title":"Genome Res"},{"issue":"23","key":"10618_CR21","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","volume":"38","author":"PA Chaumeil","year":"2022","unstructured":"Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics. 2022;38(23):5315\u20136.","journal-title":"Bioinformatics"},{"issue":"1","key":"10618_CR22","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1039\/C5AY02550H","volume":"8","author":"L Pritchard","year":"2016","unstructured":"Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods-Uk. 2016;8(1):12\u201324.","journal-title":"Anal Methods-Uk"},{"issue":"1","key":"10618_CR23","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1099\/ijsem.0.002516","volume":"68","author":"J Chun","year":"2018","unstructured":"Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol. 2018;68(1):461\u20136.","journal-title":"Int J Syst Evol Microbiol"},{"key":"10618_CR24","unstructured":"Team RC. R: A language and environment for statistical computing. R Foundation for Statistical Computing; 2017: Available at: http:\/\/www.r-project.org\/index.html."},{"key":"10618_CR25","unstructured":"Kassambara A, Mundt F. factoextra : Extract and Visualize the Results of Multivariate Data Analyses. 2020:Available at: http:\/\/www.sthda.com\/english\/rpkgs\/factoextra."},{"issue":"14","key":"10618_CR26","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068\u20139.","journal-title":"Bioinformatics"},{"key":"10618_CR27","doi-asserted-by":"crossref","unstructured":"Katz LS, Griswold T, Morrison SS, Caravas JA, Zhang S, den Bakker HC, et al. Mashtree: a rapid comparison of whole genome sequence files. J Open Source Softw. 2019;4(44).","DOI":"10.21105\/joss.01762"},{"issue":"8","key":"10618_CR28","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","volume":"34","author":"J Huerta-Cepas","year":"2017","unstructured":"Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol. 2017;34(8):2115\u201322.","journal-title":"Mol Biol Evol"},{"issue":"D1","key":"10618_CR29","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","volume":"47","author":"J Huerta-Cepas","year":"2019","unstructured":"Huerta-Cepas J, Szklarczyk D, Heller D, Hernandez-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47(D1):D309\u201314.","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10618_CR30","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s40168-021-01213-8","volume":"10","author":"Z Zhou","year":"2022","unstructured":"Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, Cowley ES, et al. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome. 2022;10(1):33.","journal-title":"Microbiome"},{"issue":"7","key":"10618_CR31","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/AAC.00419-13","volume":"57","author":"AG McArthur","year":"2013","unstructured":"McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013;57(7):3348\u201357.","journal-title":"Antimicrob Agents Chemother"},{"issue":"D1","key":"10618_CR32","first-page":"D517","volume":"48","author":"BP Alcock","year":"2020","unstructured":"Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48(D1):D517\u201325.","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"10618_CR33","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W293\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"10618_CR34","doi-asserted-by":"publisher","first-page":"6290","DOI":"10.1128\/AEM.02308-14","volume":"80","author":"C Milani","year":"2014","unstructured":"Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F, Mangifesta M, et al. Genomic encyclopedia of type strains of the Genus Bifidobacterium. Appl Environ Microbiol. 2014;80(20):6290\u2013302.","journal-title":"Appl Environ Microbiol"},{"key":"10618_CR35","unstructured":"Ramsey M, Hartke A, Huycke M. The physiology and metabolism of enterococci. In: Gilmore MS, Clewell DB, Ike Y, Shankar N, editors. Enterococci: from commensals to leading causes of drug resistant infection. Boston:\u00a0Massachusetts Eye and Ear Infirmary; 2014."},{"issue":"1","key":"10618_CR36","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1186\/s12864-017-3955-4","volume":"18","author":"GA Lugli","year":"2017","unstructured":"Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, et al. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics. 2017;18(1):568.","journal-title":"BMC Genomics."},{"issue":"1","key":"10618_CR37","doi-asserted-by":"publisher","first-page":"e02348","DOI":"10.1128\/mBio.02348-16","volume":"8","author":"G Wu","year":"2017","unstructured":"Wu G, Zhang C, Wu H, Wang R, Shen J, Wang L, et al. Genomic microdiversity of bifidobacterium pseudocatenulatum underlying differential strain-level responses to dietary carbohydrate intervention. mBio. 2017;8(1):e02348\u201316.","journal-title":"mBio"},{"key":"10618_CR38","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s12864-017-4388-9","volume":"19","author":"S Arboleya","year":"2018","unstructured":"Arboleya S, Bottacini F, O\u2019Connell-Motherway M, Ryan CA, Ross RP, van Sinderen D, et al. Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics. 2018;19:33.","journal-title":"BMC Genomics"},{"key":"10618_CR39","doi-asserted-by":"publisher","first-page":"15782","DOI":"10.1038\/srep15782","volume":"5","author":"C Milani","year":"2015","unstructured":"Milani C, Lugli GA, Duranti S, Turroni F, Mancabelli L, Ferrario C, et al. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep-Uk. 2015;5:15782.","journal-title":"Sci Rep-Uk"},{"issue":"12","key":"10618_CR40","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1093\/protein\/gzl044","volume":"19","author":"MR Stam","year":"2006","unstructured":"Stam MR, Danchin EG, Rancurel C, Coutinho PM, Henrissat B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel. 2006;19(12):555\u201362.","journal-title":"Protein Eng Des Sel"},{"issue":"6","key":"10618_CR41","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.1128\/AEM.03453-15","volume":"82","author":"K Mewis","year":"2016","unstructured":"Mewis K, Lenfant N, Lombard V, Henrissat B. Dividing the large glycoside hydrolase family 43 into subfamilies: a motivation for detailed enzyme characterization. Appl Environ Microbiol. 2016;82(6):1686\u201392.","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"10618_CR42","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1042\/BST20150226","volume":"44","author":"N Juge","year":"2016","unstructured":"Juge N, Tailford L, Owen CD. Sialidases from gut bacteria: a mini-review. Biochem Soc Trans. 2016;44(1):166\u201375.","journal-title":"Biochem Soc Trans"},{"key":"10618_CR43","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1186\/s13068-019-1411-1","volume":"12","author":"C Luo","year":"2019","unstructured":"Luo C, Li Y, Chen Y, Fu C, Long W, Xiao X, et al. Bamboo lignocellulose degradation by gut symbiotic microbiota of the bamboo snout beetle Cyrtotrachelus buqueti. Biotechnol Biofuels. 2019;12:70.","journal-title":"Biotechnol Biofuels"},{"issue":"1","key":"10618_CR44","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1038\/s42003-023-04808-z","volume":"6","author":"B Salamaga","year":"2023","unstructured":"Salamaga B, Turner RD, Elsarmane F, Galley NF, Kulakauskas S, Mesnage S. A moonlighting role for LysM peptidoglycan binding domains underpins Enterococcus faecalis daughter cell separation. Commun Biol. 2023;6(1):428.","journal-title":"Commun Biol"},{"issue":"4","key":"10618_CR45","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1038\/nbt1298","volume":"25","author":"QP Liu","year":"2007","unstructured":"Liu QP, Sulzenbacher G, Yuan H, Bennett EP, Pietz G, Saunders K, et al. Bacterial glycosidases for the production of universal red blood cells. Nat Biotechnol. 2007;25(4):454\u201364.","journal-title":"Nat Biotechnol"},{"key":"10618_CR46","doi-asserted-by":"publisher","first-page":"2305","DOI":"10.3389\/fmicb.2019.02305","volume":"10","author":"MA Engevik","year":"2019","unstructured":"Engevik MA, Morra CN, Roth D, Engevik K, Spinler JK, Devaraj S, et al. Microbial metabolic capacity for intestinal folate production and modulation of host folate receptors. Front Microbiol. 2019;10:2305.","journal-title":"Front Microbiol"},{"issue":"18","key":"10618_CR47","doi-asserted-by":"publisher","first-page":"10971","DOI":"10.3390\/ijms231810971","volume":"23","author":"AG Abril","year":"2022","unstructured":"Abril AG, Quintela-Baluja M, Villa TG, Calo-Mata P, Barros-Velazquez J, Carrera M. Proteomic characterization of virulence factors and related proteins in enterococcus strains from dairy and fermented food products. Int J Mol Sci. 2022;23(18):10971.","journal-title":"Int J Mol Sci"},{"issue":"49","key":"10618_CR48","doi-asserted-by":"publisher","first-page":"38813","DOI":"10.1074\/jbc.M007093200","volume":"275","author":"JL Carlos","year":"2000","unstructured":"Carlos JL, Paetzel M, Brubaker G, Karla A, Ashwell CM, Lively MO, et al. The role of the membrane-spanning domain of type I signal peptidases in substrate cleavage site selection. J Biol Chem. 2000;275(49):38813\u201322.","journal-title":"J Biol Chem"},{"key":"10618_CR49","doi-asserted-by":"publisher","first-page":"18964","DOI":"10.1073\/pnas.0809584105","volume":"105","author":"DA Sela","year":"2008","unstructured":"Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci. 2008;105:18964\u20139.","journal-title":"Proc Natl Acad Sci"},{"key":"10618_CR50","doi-asserted-by":"publisher","first-page":"13517","DOI":"10.1038\/srep13517","volume":"5","author":"D Garrido","year":"2015","unstructured":"Garrido D, Ruiz-Moyano S, Lemay DG, Sela DA, German JB, Mills DA. Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria. Sci Rep. 2015;5:13517.","journal-title":"Sci Rep"},{"key":"10618_CR51","doi-asserted-by":"publisher","DOI":"10.1038\/srep38560","volume":"6","author":"K James","year":"2016","unstructured":"James K, Motherway MO, Bottacini F, van Sinderen D. Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways. Sci Rep. 2016;6: 38560.","journal-title":"Sci Rep"},{"key":"10618_CR52","doi-asserted-by":"publisher","first-page":"35045","DOI":"10.1038\/srep35045","volume":"6","author":"D Garrido","year":"2016","unstructured":"Garrido D, Ruiz-Moyano S, Kirmiz N, Davis JC, Totten SM, Lemay DG, et al. A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp longum SC596. Sci Rep-Uk. 2016;6:35045.","journal-title":"Sci Rep-Uk"},{"issue":"4","key":"10618_CR53","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1128\/AEM.03500-15","volume":"82","author":"C Milani","year":"2016","unstructured":"Milani C, Turroni F, Duranti S, Lugli GA, Mancabelli L, Ferrario C, et al. Genomics of the genus Bifidobacterium reveals species-specific adaptation to the glycan-rich gut environment. Appl Environ Microbiol. 2016;82(4):980\u201391.","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"10618_CR54","doi-asserted-by":"publisher","first-page":"e0034322","DOI":"10.1128\/msystems.00343-22","volume":"7","author":"AA Arzamasov","year":"2022","unstructured":"Arzamasov AA, Nakajima A, Sakanaka M, Ojima MN, Katayama T, Rodionov DA, et al. Human milk oligosaccharide utilization in intestinal bifidobacteria is governed by global transcriptional regulator NagR. mSystems. 2022;7(5):e0034322.","journal-title":"mSystems"},{"issue":"5","key":"10618_CR55","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/mBio.00928-17","volume":"8","author":"K Nishiyama","year":"2017","unstructured":"Nishiyama K, Yamamoto Y, Sugiyama M, Takaki T, Urashima T, Fukiya S, et al. Bifidobacterium bifidum extracellular sialidase enhances adhesion to the mucosal surface and supports carbohydrate assimilation. MBio. 2017;8(5):10\u2013128.","journal-title":"MBio"},{"key":"10618_CR56","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.anaerobe.2018.05.007","volume":"52","author":"K Nishiyama","year":"2018","unstructured":"Nishiyama K, Nagai A, Uribayashi K, Yamamoto Y, Mukai T, Okada N. Two extracellular sialidases from Bifidobacterium bifidum promote the degradation of sialyl-oligosaccharides and support the growth of Bifidobacterium breve. Anaerobe. 2018;52:22\u20138.","journal-title":"Anaerobe"},{"issue":"10","key":"10618_CR57","doi-asserted-by":"publisher","first-page":"e0041022","DOI":"10.1128\/aem.00410-22","volume":"88","author":"B Li","year":"2022","unstructured":"Li B, Chen D, Lin F, Wu C, Cao L, Chen H, et al. Genomic island-mediated horizontal transfer of the erythromycin resistance gene erm(X) among Bifidobacteria. Appl Environ Microbiol. 2022;88(10):e0041022.","journal-title":"Appl Environ Microbiol"},{"issue":"8","key":"10618_CR58","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1016\/j.tim.2021.01.003","volume":"29","author":"M Cunningham","year":"2021","unstructured":"Cunningham M, Azcarate-Peril MA, Barnard A. Shaping the future of probiotics and prebiotics. Trends Microbiol. 2021;29(8):667\u201385.","journal-title":"Trends Microbiol"},{"issue":"12","key":"10618_CR59","doi-asserted-by":"publisher","first-page":"e1005300","DOI":"10.1371\/journal.pcbi.1005300","volume":"12","author":"R Berlemont","year":"2016","unstructured":"Berlemont R, Martiny AC. Glycoside hydrolases across environmental microbial communities. PLoS Comput Biol. 2016;12(12):e1005300.","journal-title":"PLoS Comput Biol"},{"key":"10618_CR60","doi-asserted-by":"publisher","first-page":"118","DOI":"10.3390\/nu3010118","volume":"1","author":"M Rossi","year":"2011","unstructured":"Rossi M, Amaretti A, Raimondi S. Folate production by probiotic bacteria. Nutrients. 2011;1:118\u201334.","journal-title":"Nutrients."},{"key":"10618_CR61","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.micres.2016.12.009","volume":"196","author":"Z Zhong","year":"2017","unstructured":"Zhong Z, Zhang W, Song Y, Liu W, Xu H, Xi X, et al. Comparative genomic analysis of the genus Enterococcus. Microbiol Res. 2017;196:95\u2013105.","journal-title":"Microbiol Res"},{"key":"10618_CR62","doi-asserted-by":"publisher","first-page":"46","DOI":"10.3389\/fnut.2018.00046","volume":"5","author":"E \u00d6zcan","year":"2018","unstructured":"\u00d6zcan E, Sela DAS. Inefficient metabolism of the human milk oligosaccharides lacto-N-tetraose and lacto-N-neotetraose shifts Bifidobacterium longum subsp infantis physiology. Front Nutr. 2018;5:46.","journal-title":"Front Nutr"},{"issue":"61","key":"10618_CR63","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1097\/MPG.0000000000000889","volume":"2015","author":"BJ Marriage","year":"2015","unstructured":"Marriage BJ, Buck RH, Goehring KC, Oliver JS, Williams JA. Infants fed a lower calorie formula with 2\u2019FL show growth and 2\u2019FL uptake like breast-fed infants. J Pediatr Gastroenterol Nutr. 2015;2015(61):649\u201358.","journal-title":"J Pediatr Gastroenterol Nutr"},{"issue":"Suppl 1","key":"10618_CR64","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00394-018-1703-4","volume":"57","author":"MH Mohajeri","year":"2018","unstructured":"Mohajeri MH, Brummer RJM, Rastall RA, Weersma RK, Harmsen HJM, Faas M, et al. The role of the microbiome for human health: from basic science to clinical applications. Eur J Nutr. 2018;57(Suppl 1):1\u201314.","journal-title":"Eur J Nutr"},{"key":"10618_CR65","doi-asserted-by":"publisher","first-page":"1319873","DOI":"10.3389\/fnut.2023.1319873","volume":"10","author":"MRZ Capeding","year":"2023","unstructured":"Capeding MRZ, Phee LCM, Ming C, Noti M, Vidal K, Le Carrou G, et al. Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines. Front Nutr. 2023;10:1319873.","journal-title":"Front Nutr"},{"issue":"10","key":"10618_CR66","doi-asserted-by":"publisher","first-page":"5860","DOI":"10.3390\/ijerph20105860","volume":"20","author":"T Nyanhanda","year":"2023","unstructured":"Nyanhanda T, Mwanri L, Mude W. Double burden of malnutrition: a population level comparative cross-sectional study across three Sub-Saharan African Countries-Malawi, Namibia and Zimbabwe. Int J Environ Res Public Health. 2023;20(10):5860.","journal-title":"Int J Environ Res Public Health"},{"issue":"1","key":"10618_CR67","doi-asserted-by":"publisher","first-page":"3554","DOI":"10.1038\/s41467-023-39285-9","volume":"14","author":"F Fontaine","year":"2023","unstructured":"Fontaine F, Turjeman S, Callens K, Koren O. The intersection of undernutrition, microbiome, and child development in the first years of life. Nat Commun. 2023;14(1):3554.","journal-title":"Nat Commun"},{"issue":"1","key":"10618_CR68","doi-asserted-by":"publisher","first-page":"15919","DOI":"10.1038\/s41598-020-72792-z","volume":"10","author":"BE Zabel","year":"2020","unstructured":"Zabel BE, Gerdes S, Evans KC, Nedveck D, Singles SK, Volk B, et al. Strain-specific strategies of 2\u2032-fucosyllactose, 3-fucosyllactose, and difucosyllactose assimilation by Bifidobacterium longum subsp. infantis Bi-26 and ATCC 15697. Scientific Reports. 2020;10(1):15919.","journal-title":"Scientific Reports"},{"issue":"3","key":"10618_CR69","doi-asserted-by":"publisher","first-page":"e02894","DOI":"10.1128\/AEM.02894-16","volume":"83","author":"S Duranti","year":"2017","unstructured":"Duranti S, Lugli GA, Mancabelli L, Turroni F, Milani C, Mangifesta M, et al. Prevalence of antibiotic resistance genes among human gut- derived bifidobacteria. Appl Environ Microbiol. 2017;83(3):e02894\u201316.","journal-title":"Appl Environ Microbiol"},{"issue":"4","key":"10618_CR70","doi-asserted-by":"publisher","first-page":"e202201637","DOI":"10.26508\/lsa.202201637","volume":"6","author":"V Rozman","year":"2023","unstructured":"Rozman V, Mohar Lorbeg P, Treven P, Accetto T, Jane\u017ei\u010d S, Rupnik M, et al. Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteria. Life Sci Alliance. 2023;6(4):e202201637.","journal-title":"Life Sci Alliance"},{"issue":"7","key":"10618_CR71","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1179\/2047773215Y.0000000030","volume":"109","author":"F Prestinaci","year":"2015","unstructured":"Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health. 2015;109(7):309\u201318.","journal-title":"Pathog Glob Health"},{"issue":"3","key":"10618_CR72","doi-asserted-by":"publisher","first-page":"743","DOI":"10.14202\/vetworld.2022.743-749","volume":"15","author":"ME Velazquez-Meza","year":"2022","unstructured":"Velazquez-Meza ME, Galarde-L\u00f3pez M, Carrillo-Quir\u00f3z B, Alpuche-Aranda CM. Antimicrobial resistance: one health approach. Vet World. 2022;15(3):743\u20139.","journal-title":"Vet World"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10618-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-024-10618-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10618-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T01:27:11Z","timestamp":1721870831000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-024-10618-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,25]]},"references-count":72,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["10618"],"URL":"https:\/\/doi.org\/10.1186\/s12864-024-10618-2","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,25]]},"assertion":[{"value":"29 April 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 July 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The research adhered to the guidelines outlined in the Declaration of Helsinki, where the participants\u2019 mothers were adequately informed about the study before providing their written consent for their infants to participate. Additionally, the study was initiated following ethical approval from multiple committees, including the Harare City Council Ethics Committee (3\/7), the Joint Research Ethics Committee for the University of Zimbabwe Faculty of Medicine and Health Science and Parirenyatwa Group of Hospitals (353\/2021), Medical Research Council in Zimbabwe (MRCZ A\/2832), and the Research Council of Zimbabwe reference number 04694.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The co-authors consented to this manuscript being published.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interest"}}],"article-number":"718"}}