Turroni F, Milani C, Duranti S, Lugli GA, Bernasconi S, Margolles A, et al. The infant gut microbiome as a microbial organ influencing host well-being. Ital J Pediatr. 2020;46:1–13.
Google Scholar
Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med. 2016;8:343ra82–343ra82.
Google Scholar
Akagawa S, Tsuji S, Onuma C, Akagawa Y, Yamaguchi T, Yamagishi M, et al. Effect of delivery mode and nutrition on gut microbiota in neonates. Ann Nutr Metab. 2019;74:132–9.
Google Scholar
Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 2018;555:210–5.
Vellend M, Srivastava DS, Anderson KM, Brown CD, Jankowski JE, Kleynhans EJ, et al. Assessing the relative importance of neutral stochasticity in ecological communities. Oikos. 2014;123:1420–30.
Google Scholar
Fukami T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu Rev Ecol Evol Syst. 2015;46:1–23.
Google Scholar
Fukami T, Nakajima M. Community assembly: Alternative stable states or alternative transient states? Ecol Lett. 2011;14:973–84.
Google Scholar
Sprockett D, Fukami T, Relman DA. Role of priority effects in the early-life assembly of the gut microbiota. Nat Rev Gastroenterol Hepatol. 2018;15:197–205.
Google Scholar
Debray R, Herbert RA, Jaffe AL, Crits-Christoph A, Power ME, Koskella B. Priority effects in microbiome assembly. Nat Rev Microbiol. 2022;20:109–21.
Google Scholar
Tannock GW, Lawley B, Munro K, Pathmanathan SG, Zhou SJ, Makrides M, et al. Comparison of the compositions of the stool microbiotas of infants fed goat milk formula, cow milk-based formula, or breast milk. Appl Environ Microbiol. 2013;79:3040–8.
Google Scholar
Matsuki T, Yahagi K, Mori H, Matsumoto H, Hara T, Tajima S, et al. A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nat Commun. 2016;7:11939.
Google Scholar
Sakanaka M, Hansen ME, Gotoh A, Katoh T, Yoshida K, Odamaki T, et al. Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis. Sci Adv. 2019;5:eaaw7696.
Google Scholar
Engfer MB, Stahl B, Finke B, Sawatzki G, Daniel H. Human milk oligosaccharides are resistant to enzymatic hydrolysis in the upper gastrointestinal tract. Am J Clin Nutr. 2000;71:1589–96.
Google Scholar
Macrobal A, Sonnenburg JL. Human milk oligosaccharide consumption by intestinal microbiota. Clin Microbiol Infect. 2012;18:12–15.
Google Scholar
Macrobal A, Barboza M, Froehlich JW, Block DE, German JB, Lebrilla CB, et al. Consumption of human milk oligosaccharides by gut-related microbes. J Agric Food Chem. 2010;58:5334–40.
Google Scholar
Sakanaka M, Gotoh A, Yoshida K, Odamaki T, Koguchi H, Xiao JZ, et al. Varied pathways of infant gut-associated Bifidobacterium to assimilate human milk oligosaccharides: prevalence of the gene set and its correlation with bifidobacteria-rich microbiota formation. Nutrients. 2020;12:71.
Google Scholar
Katayama T. Host-derived glycans serve as selected nutrients for the gut microbe: human milk oligosaccharides and bifidobacteria. Biosci Biotechnol Biochem. 2016;80:621–32.
Google Scholar
Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A, Merusi P, et al. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl Environ Microbiol. 2009;75:1534–45.
Google Scholar
Gore C, Munro K, Lay C, Bibiloni R, Morris J, Woodcock A, et al. Bifidobacterium pseudocatenulatum is associated with atopic eczema: A nested case-control study investigating the fecal microbiota of infants. J Allergy Clin Immunol. 2008;121:135–40.
Google Scholar
Lewis ZT, Mills DA. Differential establishment of bifidobacteria in the breastfed infant gut. Nestle Nutr Inst Work Ser. 2017;88:149–59.
Google Scholar
Tannock GW, Lee PS, Wong KH, Lawley B. Why don’t all infants have bifidobacteria in their stool? Front Microbiol. 2016;7:6–10.
Google Scholar
Reyman M, van Houten MA, van Baarle D, Bosch AATM, Man WH, Chu MLJN, et al. Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life. Nat Commun. 2019;10:1–12.
Google Scholar
Underwood MA, Kalanetra KM, Bokulich NA, Lewis ZT, Mirmiran M, Tancredi DJ, et al. A comparison of two probiotic strains of bifidobacteria in preterm infants. J Pediatr. 2013;163:1585–91.
Google Scholar
Plummer EL, Bulach DM, Murray GL, Jacobs SE, Tabrizi SN, Garland SM. Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial. BMC Microbiol. 2018;18:1–8.
Google Scholar
Kitajima H, Sumida Y, Tanaka R, Yuki N, Takayama H, Fujimura M. Early administration of Bifidobacterium breve to preterm infants: Randomised controlled trial. Arch Dis Child Fetal Neonatal Ed. 1997;76:101–7.
Google Scholar
Ojima MN, Yoshida K, Sakanaka M, Jiang L, Odamaki T, Katayama T. Ecological and molecular perspectives on responders and non-responders to probiotics and prebiotics. Curr Opin Biotechnol. 2022;73:108–20.
Google Scholar
Suez J, Zmora N, Segal E, Elinav E. The pros, cons, and many unknowns of probiotics. Nat Med. 2019;25:716–29.
Google Scholar
Costeloe K, Hardy P, Juszczak E, Wilks M, Millar MR. Bifidobacterium breve BBG-001 in very preterm infants: A randomised controlled phase 3 trial. Lancet. 2016;387:649–60.
Google Scholar
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33:5691–702.
Google Scholar
Katoh T, Ojima MN, Sakanaka M, Ashida H, Gotoh A, Katayama T. Enzymatic adaptation of Bifidobacterium bifidum to host glycans, viewed from glycoside hydrolyases and carbohydrate-binding modules. Microorganisms. 2020;8:481.
Google Scholar
Egan M, Motherway MO, Kilcoyne M, Kane M, Joshi L, Ventura M, et al. Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium. BMC Microbiol. 2014;14:1–14.
Google Scholar
Higgins MA, Ryan KS. Generating a fucose permease deletion mutant in Bifidobacterium longum subspecies infantis ATCC 15697. Anaerobe. 2021;68:102320.
Google Scholar
O’Connell Motherway M, Kinsella M, Fitzgerald GF, van Sinderen D. Transcriptional and functional characterization of genetic elements involved in galacto-oligosaccharide utilization by Bifidobacterium breve UCC2003. Micro Biotechnol. 2013;6:67–79.
Google Scholar
Yoshida E, Sakurama H, Kiyohara M, Nakajima M, Kitaoka M, Ashida H, et al. Bifidobacterium longum subsp. infantis uses two different β-galactosidases for selectively degrading type-1 and type-2 human milk oligosaccharides. Glycobiology. 2012;22:361–8.
Google Scholar
Vannette RL, Fukami T. Historical contingency in species interactions: Towards niche-based predictions. Ecol Lett. 2014;17:115–24.
Google Scholar
Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe. 2015;17:690–703.
Google Scholar
Pu Z, Jiang L. Dispersal among local communities does not reduce historical contingencies during metacommunity assembly. Oikos. 2015;124:1327–36.
Google Scholar
Chase JM. Community assembly: when should history matter? Oecologia. 2003;136:489–98.
Google Scholar
Schröder A, Persson L, De Roos AM. Direct experimental evidence for alternative stable states: A review. Oikos. 2005;110:3–19.
Google Scholar
Asakuma S, Hatakeyama E, Urashima T, Yoshida E, Katayama T, Yamamoto K, et al. Physiology of consumption of human milk oligosaccharides by infant gut-associated bifidobacteria. J Biol Chem. 2011;286:34583–92.
Google Scholar
Gotoh A, Katoh T, Sakanaka M, Ling Y, Yamada C, Asakuma S, et al. Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum. Sci Rep. 2018;8:13958.
Google Scholar
Ashida H, Miyake A, Kiyohara M, Wada J, Yoshida E, Kumagai H, et al. Two distinct α-l-fucosidases from Bifidobacterium bifidum are essential for the utilization of fucosylated milk oligosaccharides and glycoconjugates. Glycobiology. 2009;19:1010–7.
Google Scholar
Roger LC, Costabile A, Holland DT, Hoyles L, McCartney AL. Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life. Microbiology. 2010;156:3329–41.
Google Scholar
Avershina E, Storrø O, Øien T, Johnsen R, Wilson R, Egeland T, et al. Bifidobacterial succession and correlation networks in a large unselected cohort of mothers and their children. Appl Environ Microbiol. 2013;79:497–507.
Google Scholar
Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, et al. Diversity of bifidobacteria within the infant gut microbiota. PLoS One. 2012;7:20–4.
Google Scholar
James K, Bottacini F, Contreras JIS, Vigoureux M, Egan M, Motherway MO, et al. Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal. Sci Rep. 2019;9:1–20.
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 Nutr. 2020;7:1–16.
Google Scholar
Sprockett D, Martin M, Costello E, Burns A, Holmes S, Gurven M, et al. Microbiota assembly, structure, and dynamics among tsimane horticulturalists of the Bolivian Amazon. Nat Commun. 2019;11:1–14.
Laursen MF, Sakanaka M, von Burg N, Mörbe U, Andersen D, Moll JM, et al. Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. Nat Microbiol. 2021;6:1367–82.
Google Scholar
Meng D, Sommella E, Salviati E, Campiglia P, Ganguli K, Djebali K, et al. Indole-3-lactic acid, a metabolite of tryptophan, secreted by Bifidobacterium longum subspecies infantis is anti-inflammatory in the immature intestine. Pediatr Res. 2020;88:209–17.
Google Scholar
Bunesova V, Lacroix C, Schwab C. Fucosyllactose and l-fucose utilization of infant Bifidobacterium longum and Bifidobacterium kashiwanohense. BMC Microbiol. 2016;16:248.
Google Scholar
Ruiz-Moyano S, Totten SM, Garrido D, Smilowitz JT, Bruce German J, Lebrilla CB, et al. Variation in consumption of human milk oligosaccharides by infant gut-associated strains of Bifidobacterium breve. Appl Environ Microbiol. 2013;79:6040–9.
Google Scholar
Lawson MAE, O’Neill IJ, Kujawska M, Gowrinadh Javvadi S, Wijeyesekera A, Flegg Z, et al. Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. ISME J. 2020;14:635–48.
Google Scholar
Schwab C, Ruscheweyh HJ, Bunesova V, Pham VT, Beerenwinkel N, Lacroix C. Trophic interactions of infant bifidobacteria and Eubacterium hallii during l-fucose and fucosyllactose degradation. Front Microbiol. 2017;8:1–14.
Google Scholar
Engels C, Ruscheweyh HJ, Beerenwinkel N, Lacroix C, Schwab C. The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation. Front Microbiol. 2016;7:1–12.
Google Scholar
Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, et al. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe. 2011;10:507–14.
Google Scholar
Vatanen T, Kostic AD, D’Hennezel E, Siljander H, Franzosa EA, Yassour M, et al. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016;165:842–53.
Google Scholar
Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, et al. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018;562:589–94.
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;25:324–335.e4.
Google Scholar
Martín R, Langa S, Reviriego C, Jiménez E, Marín ML, Xaus J, et al. Human milk is a source of lactic acid bacteria for the infant gut. J Pediatr. 2003;143:754–8.
Google Scholar
Martín R, Jiménez E, Heilig H, Fernández L, Marín ML, Zoetendal EG, et al. Isolation of bifidobacteria from breast milk and assessment of the bifidobacterial population by PCR-denaturing gradient gel electrophoresis and quantitative real-time PCR. Appl Environ Microbiol. 2009;75:965–9.
Google Scholar
Heikkilä MP, Saris PEJ. Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. J Appl Microbiol. 2003;95:471–8.
Google Scholar
Li Y, Shimizu T, Hosaka A, Kaneko N, Ohtsuka Y, Yamashiro Y. Effects of Bifidobacterium breve supplementation on intestinal flora of low birth weight infants. Pediatr Int. 2004;46:509–15.
Google Scholar
Nishimoto M, Kitaoka M. Practical preparation of lacto-N-biose I, a candidate for the bifidus factor in human milk. Biosci Biotechnol Biochem. 2007;71:2101–4.
Google Scholar
Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol. 2002;52:2141–6.
Google Scholar
Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature. 2016;533:543–6.
Google Scholar
Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y. Arita M. DFAST and DAGA: Web-based integrated genome annotation tools and resources. Biosci Microbiota, Food Heal. 2016;35:173–84.
Google Scholar
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42:206–14.
Google Scholar
Price MN, Arkin AP. PaperBLAST: Text-mining papers for information about homologs. bioRxiv. 2017;2:1–10.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:490–5.
Google Scholar
Saier MH, Reddy VS, Tsu BV, Ahmed MS, Li C, Moreno-Hagelsieb G. The Transporter Classification Database (TCDB): Recent advances. Nucleic Acids Res. 2016;44:D372–9.
Google Scholar
Martínez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, et al. Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota. Appl Environ Microbiol. 2009;75:4175–84.
Google Scholar
Anumula KR. Advances in fluorescence derivatization methods for high-performance liquid chromatographic analysis of glycoprotein carbohydrates. Anal Biochem. 2006;350:1–23.
Google Scholar
Cohenford MA, Abraham A, Abraham J, Dain JA. Colorimetric assay for free and bound l-fucose. Anal Biochem. 1989;177:172–7.
Google Scholar
Kato K, Odamaki T, Mitsuyama E, Sugahara H, Xiao JZ, Osawa R. Age-related changes in the composition of gut Bifidobacterium species. Curr Microbiol. 2017;74:987–95.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 2011;17:10–12.
Google Scholar
Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20:1–13.
Google Scholar
Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: Estimating species abundance in metagenomics data. PeerJ Comput Sci. 2017;2017:1–17.
Google Scholar
Milani C, Lugli GA, Fontana F, Mancabelli L, Alessandri G, Longhi G, et al. METAnnotatorX2: A comprehensive tool for deep and shallow metagenomic data set analyses. mSystems. 2021;6:1–15.
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2019.
Source: Ecology - nature.com
