Bifidobacterium infantis utilizes N-acetylglucosamine-containing human milk oligosaccharides as a nitrogen source

References

• Cilieborg MS, Boye M, Sangild PT. Bacterial Colonization and Gut Development in Preterm Neonates. Early Hum Dev. 2012;88(SUPPL. 1). doi:10.1016/j.earlhumdev.2011.12.027.
   PubMedGoogle Scholar
• Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, Reading NC, Villablanca EJ, Wang S, Mora JR, et al. Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota. Cell. 2012;149(7). doi:10.1016/j.cell.2012.04.037.
   PubMed Web of Science ®Google Scholar
• Bode L. Human Milk Oligosaccharides: Every Baby Needs a Sugar Mama. Glycobiology. 2012;22(9):1147–15. doi:https://doi.org/10.1093/glycob/cws074.
   PubMed Web of Science ®Google Scholar
• German J, Freeman S, Lebrilla C, Mills D Human Milk Oligosaccharides: Evolution, Structures and Bioselectivity as Substrates for Intestinal Bacteria. In Nestle Nutrition Workshop Series: Pediatric Program; 2008; Vol. 62. 10.1159/000146322.
   Google Scholar
• Sela DA; Chapman J; Adeuya A; Kim JH; Chen F; Whitehead TR; Lapidus A; Rokhsar DS; Lebrilla CB; German JB; Price NP; Richardson PM; Mills DA. The Genome Sequence of Bifidobacterium Longum Subsp. Infantis Reveals Adaptations for Milk Utilization within the Infant Microbiome. Proc Natl Acad Sci U S A. 2008;105(48):18964–18969. doi:10.1073/pnas.0809584105.
   PubMed Web of Science ®Google Scholar
• LoCascio RG; Desai P; Sela DA; Weimer B; Mills DA. Broad Conservation of Milk Utilization Genes in Bifidobacterium Longum Subsp. Infantis as Revealed by Comparative Genomic Hybridization. Appl Environ Microb. 2010;76(22):7373–7381. doi:10.1128/AEM.00675-10.
   PubMed Web of Science ®Google Scholar
• Duar RM, Casaburi G, Mitchell RD, Scofield LNC, Ortega Ramirez CA, Barile D, Henrick BM, Frese SA. Comparative Genome Analysis of Bifidobacterium Longum Subsp. Infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics. Nutrients. 2020;12(11). doi:10.3390/nu12113247.
   PubMed Web of Science ®Google Scholar
• Merrick MJ, Edwards RA. Nitrogen Control in Bacteria. Microbiol Rev. 1995;59(4):604–622. doi:https://doi.org/10.1128/mr.59.4.604-622.1995.
   PubMedGoogle Scholar
• Schell MA; Karmirantzou M; Snel B; Vilanova D; Berger B; Pessi G; Zwahlen MC; Desiere F; Bork P; Delley M; Pridmore RD; Arigoni F. The Genome Sequence of Bifidobacterium Longum Reflects Its Adaptation to the Human Gastrointestinal Tract. Proc Natl Acad Sci U S A. 2002;99(22):14422–14427. doi:10.1073/pnas.212527599.
   PubMed Web of Science ®Google Scholar
• Huergo LF; Dixon R. The Emergence of 2-Oxoglutarate as a Master Regulator Metabolite. Microbiol Mol Biol R. 2015;79(4):419–435. doi:10.1128/mmbr.00038-15.
   PubMed Web of Science ®Google Scholar
• Yan D, Lenz P, Hwa T. Overcoming Fluctuation and Leakage Problems in the Quantification of Intracellular 2-Oxoglutarate Levels in Escherichia Coli. Appl Environ Microb. 2011;77:19. doi:10.1128/AEM.05257-11.
   Web of Science ®Google Scholar
• Yuan J, Doucette CD, Fowler WU, Feng XJ, Piazza M, Rabitz HA, Wingreen NS, Rabinowitz JD. Metabolomics-Driven Quantitative Analysis of Ammonia Assimilation in E. Coli. Molecular Systems Biology. 2009;5:5. doi:10.1038/msb.2009.60.
   Web of Science ®Google Scholar
• Oliveira MAS, Gerhardt ECM, Huergo LF, Souza EM, Pedrosa FO, Chubatsu LS. 2-Oxoglutarate Levels Control Adenosine Nucleotide Binding by Herbaspirillum Seropedicae PII Proteins. FEBS J. 2015;282:24. doi:10.1111/febs.13542.
   Web of Science ®Google Scholar
• Zhang CC, Zhou CZ, Burnap RL, Peng L. Carbon/Nitrogen Metabolic Balance: Lessons from Cyanobacteria. Trends In Plant Science. 2018;23:1116–1130. doi:10.1016/j.tplants.2018.09.008.
   PubMed Web of Science ®Google Scholar
• Brauer MJ, Yuan J, Bennett BD, Lu W, Kimball E, Botstein D, Rabinowitz JD. Conservation of the Metabolomic Response to Starvation across Two Divergent Microbes. Proc Natl Acad Sci U S A. 2006;103(51). doi:10.1073/pnas.0609508103.
   PubMed Web of Science ®Google Scholar
• Chubukov V, Sauer U. Environmental Dependence of Stationary-Phase Metabolism in Bacillus Subtilis and Escherichia Coli. Appl Environ Microbiol. 2014;80(9):2901–2909. doi:10.1128/AEM.00061-14.
   PubMed Web of Science ®Google Scholar
• Thum C, Wall CR, Weiss GA, Wang W, Szeto IMY, Day L. Changes in Hmo Concentrations throughout Lactation: Influencing Factors, Health Effects and Opportunities. Nutrients. 2021;13(7):2272. doi:https://doi.org/10.3390/nu13072272.
   PubMed Web of Science ®Google Scholar
• Korem Kohanim Y, Levi D, Jona G, Towbin BD, Bren A, Alon U. A Bacterial Growth Law out of Steady State. Cell Rep. 2018;23(10):2891–2900. doi:10.1016/j.celrep.2018.05.007.
   PubMed Web of Science ®Google Scholar
• Özcan E, Sela DA. Inefficient Metabolism of the Human Milk Oligosaccharides Lacto-N-Tetraose and Lacto-N-Neotetraose Shifts Bifidobacterium Longum Subsp. Infantis Physiology. Front Nutr. 2018;5:5. doi:https://doi.org/10.3389/fnut.2018.00046.
   PubMed Web of Science ®Google Scholar
• Garrido D, Ruiz-Moyano S, Mills DA. Release and Utilization of N-Acetyl-d-Glucosamine from Human Milk Oligosaccharides by Bifidobacterium Longum Subsp. Infantis. Anaerobe. 2012;18(4):430–435. doi:10.1016/j.anaerobe.2012.04.012.
   PubMed Web of Science ®Google Scholar
• Amon J, Titgemeyer F, Burkovski A. Common patterns – unique features: nitrogen metabolism and regulation in Gram-positive bacteria. FEMS Microbiol Rev. 2010 July 1;34(4):588–605. doi:https://doi.org/10.1111/j.1574-6976.2010.00216.x. Blackwell Publishing Ltd.
   PubMed Web of Science ®Google Scholar
• Schimmel P, Kleinjans L, Bongers RS, Knol J, Belzer C. Breast Milk Urea as a Nitrogen Source for Urease Positive Bifidobacterium Infantis. FEMS Microbiol Ecol. 2021;97:3. doi:10.1093/femsec/fiab019.
   Web of Science ®Google Scholar
• You X, Rani A, Özcan E, Lyu Y, Sela DA. Bifidobacterium longum subsp. infantis utilizes human milk urea to recycle nitrogen within the infant gut microbiome. Gut Microbes. 2023 Jan-Dec;15(1):2192546. doi: 10.1080/19490976.2023.2192546. PMID: 36967532; PMCID: PMC10054289.
   PubMed Web of Science ®Google Scholar
• Sela DA, Mills DA. Nursing Our Microbiota: Molecular Linkages between Bifidobacteria and Milk Oligosaccharides. Trends In Microbiology. 2010;18(7):298–307. doi:https://doi.org/10.1016/j.tim.2010.03.008.
   PubMed Web of Science ®Google Scholar
• Ferrario C, Duranti S, Milani C, Mancabelli L, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ossiprandi MC, van Sinderen D, et al. Exploring Amino Acid Auxotrophy in Bifidobacterium Bifidum PRL2010. Front Microbiol. 2015;6(NOV). doi:10.3389/fmicb.2015.01331.
   PubMedGoogle Scholar
• Wada M, Fukiya S, Suzuki A, Matsumoto N, Matsuo M, Yokota A. Methionine Utilization by Bifidobacteria: Possible Existence of a Reverse Transsulfuration Pathway. Biosci Microbiota Food Health. 2021;40(1):80–83. doi:https://doi.org/10.12938/BMFH.2020-031.
   PubMed Web of Science ®Google Scholar
• Schöpping M, Gaspar P, Neves AR, Franzén CJ, Zeidan AA. Identifying the Essential Nutritional Requirements of the Probiotic Bacteria Bifidobacterium Animalis and Bifidobacterium Longum through Genome-Scale Modeling. Npj Syst Biol Appl. 2021;7(1). doi:10.1038/s41540-021-00207-4.
   PubMed Web of Science ®Google Scholar
• Chubukov V, Gerosa L, Kochanowski K, Sauer U. Coordination of Microbial Metabolism. Nat Rev Microbiol. 2014;12(5):327–340. doi:https://doi.org/10.1038/nrmicro3238.
   PubMed Web of Science ®Google Scholar
• Wray LV, Fisher SH. The Streptomyces Coelicolor GlnR Gene Encodes a Protein Similar to Other Bacterial Response Regulators. Gene. 1993;130(1):145–150. doi:https://doi.org/10.1016/0378-1119(93)90359-B.
   PubMed Web of Science ®Google Scholar
• Walter B, Hänssler E, Kalinowski J, Burkovski A. Nitrogen Metabolism and Nitrogen Control in Corynebacteria: Variations of a Common Theme. J Mol Microbiol Biotechnol. 2006;12:1–2. doi:10.1159/000096468.
   Web of Science ®Google Scholar
• Sprouffske K, Wagner A. Growthcurver: An R Package for Obtaining Interpretable Metrics from Microbial Growth Curves. BMC Bioinform. 2016;17(1):172. doi:10.1186/s12859-016-1016-7.
   PubMedGoogle Scholar
• R Core Team. R: A Language and Environment for Statistical Computing. R Foundation For Statistical Computing, Vienna, Austria. 2020. https://ropensci.org/blog/2021/11/16/how-to-cite-r-and-r-packages/.
   Google Scholar
• Bajad SU, Lu W, Kimball EH, Yuan J, Peterson C, Rabinowitz JD. Separation and Quantitation of Water Soluble Cellular Metabolites by Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry. J Chromatogr A. 2006;1125(1):76–88. doi:10.1016/j.chroma.2006.05.019.
   PubMed Web of Science ®Google Scholar
• 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;5:5. doi:10.1038/srep13517.
   Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2. Genome Biol. 2014;15:12. doi:10.1186/s13059-014-0550-8.
   Web of Science ®Google Scholar
• Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. 2010.
   Google Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics. 2014;30:15. doi:10.1093/bioinformatics/btu170.
   Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast Gapped-Read Alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359. doi:10.1038/nmeth.1923.
   PubMed Web of Science ®Google Scholar
• Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, et al. Twelve Years of SAMtools and BCFtools. GigaScience. 2021;10(2). doi:10.1093/gigascience/giab008.
   Web of Science ®Google Scholar
• Anders S, Pyl PT, Huber W. HTSeq-A Python Framework to Work with High-Throughput Sequencing Data. Bioinformatics. 2015;31(2):166–169. doi:10.1093/bioinformatics/btu638.
   PubMed Web of Science ®Google Scholar
• Kolde R, Kolde MR. Package ‘pheatmap’. R package. 2015;1(7): 790.
   Google Scholar
• Dedon LR, Özcan E, Rani A, Sela DA. Bifidobacterium Infantis Metabolizes 2′Fucosyllactose-Derived and Free Fucose Through a Common Catabolic Pathway Resulting in 1,2-Propanediol Secretion. Front nutrition. 2020;7:7. doi:10.3389/fnut.2020.583397.
   PubMed Web of Science ®Google Scholar
• Chong J, Soufan O, Li C, Caraus I, Li S, Bourque G, Wishart DS, Xia J. MetaboAnalyst 4.0: Towards More Transparent and Integrative Metabolomics Analysis. Nucleic Acids Res. 2018;46:W1. doi:10.1093/nar/gky310.
   PubMed Web of Science ®Google Scholar
• Wickham H, Averick M, Bryan J, Chang W, McGowan L, François R, Grolemund G, Hayes A, Henry L, Hester J, et al. Welcome to the Tidyverse. J Open Source Softw. 2019;4(43). doi:10.21105/joss.01686.
   Google Scholar