Human Milk Protein-Derived Bioactive Peptides from In Vitro-Digested Colostrum Exert Antimicrobial Activities against Common Neonatal Pathogens
<p>Venn diagram and bar graph of (<b>a</b>) counts; (<b>b</b>) total chromatographic abundances (Log10) of human milk peptides identified from undigested and digested human milk samples; (<b>c</b>) Pie charts show the percentage of the total abundance of common (16% and 17%, respectively, in dark grey) and unique (84% and 83%, respectively) proteins identified in undigested (in white) and digested (in black) samples. * <span class="html-italic">p</span> = 0.005; difference in total peptide abundance between undigested and digested using related-samples Wilcoxon Signed Rank test.</p> "> Figure 2
<p>Top 10 parent proteins based on highest number of peptides that were derived in both undigested (blue) and digested (red) human milk samples.</p> "> Figure 3
<p>Heatmap and hierarchical clustering showing the similarity/differences of abundance pattern of human milk proteins that were identified using peptide profiles between undigested (U) and digested (D) samples.</p> "> Figure 4
<p>Percent change in optical density at 600 nm from the growth of common pathogenic bacteria incubated with synthesized peptides SP1-SP4. (<b>a</b>) <span class="html-italic">C. freundii</span>; (<b>b</b>) <span class="html-italic">E. coli</span>; (<b>c</b>) <span class="html-italic">K. aerogenes</span>; (<b>d</b>) <span class="html-italic">S. marcescens.</span></p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Colostrum Samples
2.2. Peptide Extraction from the Colostrum Samples
2.3. Peptide Analysis Using Liquid Chromatography and Mass Spectrometry (LC-MS)
2.4. LC-MS Data Analysis
2.5. Homology Search against Known Bioactive Peptides
2.6. Sequence-Based Prediction of Antimicrobial Peptides
2.7. Bacterial Strains and Culture Conditions
2.8. Antimicrobial Activity of Predicted Peptides
2.9. Statistical Analysis
3. Results
3.1. Comparison of Peptides Identified in Undigested and Digested Samples
3.2. Sequence-Based Prediction of Bioactive Peptides
3.3. Antimicrobial Activity of the Peptides with Predicted Antimicrobial Activities
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Alsaied, A.; Islam, N.; Thalib, L. Global incidence of necrotizing enterocolitis: A systematic review and meta-analysis. BMC Pediatr. 2020, 20, 344. [Google Scholar] [CrossRef] [PubMed]
- Altobelli, E.; Angeletti, P.M.; Verrotti, A.; Petrocelli, R. The impact of human milk on necrotizing enterocolitis: A systematic review and meta-analysis. Nutrients 2020, 12, 1322. [Google Scholar] [CrossRef] [PubMed]
- Jones, I.H.; Hall, N.J. Contemporary outcomes for infants with necrotizing enterocolitis-a systematic review. J. Pediatr. 2020, 220, 86–92.e83. [Google Scholar] [CrossRef]
- Kinstlinger, N.; Fink, A.; Gordon, S.; Levin, T.L.; Friedmann, P.; Nafday, S.; Statter, M.; Borenstein, S.H. Is necrotizing enterocolitis the same disease in term and preterm infants? J. Pediatr. Surg. 2021, 56, 1370–1374. [Google Scholar] [CrossRef]
- Liepke, C.; Zucht, H.D.; Forssmann, W.G.; Ständker, L. Purification of novel peptide antibiotics from human milk. J. Chromatogr. B Biomed. Sci. Appl. 2001, 752, 369–377. [Google Scholar] [CrossRef] [PubMed]
- Wan, J.; Cui, X.W.; Zhang, J.; Fu, Z.Y.; Guo, X.R.; Sun, L.Z.; Ji, C.B. Peptidome analysis of human skim milk in term and preterm milk. Biochem. Biophys. Res. Commun. 2013, 438, 236–241. [Google Scholar] [CrossRef]
- Deglaire, A.; De Oliveira, S.; Jardin, J.; Briard-Bion, V.; Kroell, F.; Emily, M.; Ménard, O.; Bourlieu, C.; Dupont, D. Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic digestion at the preterm newborn stage. Food Chem. 2019, 281, 294–303. [Google Scholar] [CrossRef]
- Wada, Y.; Lönnerdal, B. Bioactive peptides derived from human milk proteins: An update. Curr. Opin. Clin. Nutr. Metab. Care 2020, 23, 217–222. [Google Scholar] [CrossRef]
- Nielsen, S.D.; Liang, N.; Rathish, H.; Kim, B.J.; Lueangsakulthai, J.; Koh, J.; Qu, Y.; Schulz, H.J.; Dallas, D.C. Bioactive milk peptides: An updated comprehensive overview and database. Crit. Rev. Food Sci. Nutr. 2023, 1–20. [Google Scholar] [CrossRef]
- Dekker, P.M.; Boeren, S.; Saccenti, E.; Hettinga, K.A. Network analysis of the proteome and peptidome sheds light on human milk as a biological system. Sci. Rep. 2024, 14, 7569. [Google Scholar] [CrossRef]
- Zhou, Y.; Shan, G.; Sodergren, E.; Weinstock, G.; Walker, W.A.; Gregory, K.E. Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: A case-control study. PLoS ONE 2015, 10, e0118632. [Google Scholar] [CrossRef] [PubMed]
- Warner, B.B.; Deych, E.; Zhou, Y.; Hall-Moore, C.; Weinstock, G.M.; Sodergren, E.; Shaikh, N.; Hoffmann, J.A.; Linneman, L.A.; Hamvas, A.; et al. Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: A prospective case-control study. Lancet 2016, 387, 1928–1936. [Google Scholar] [CrossRef] [PubMed]
- Pammi, M.; Cope, J.; Tarr, P.I.; Warner, B.B.; Morrow, A.L.; Mai, V.; Gregory, K.E.; Kroll, J.S.; McMurtry, V.; Ferris, M.J.; et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: A systematic review and meta-analysis. Microbiome 2017, 5, 31. [Google Scholar] [CrossRef] [PubMed]
- Bazacliu, C.; Neu, J. Pathophysiology of necrotizing enterocolitis: An update. Curr. Pediatr. Rev. 2019, 15, 68–87. [Google Scholar] [CrossRef] [PubMed]
- Lindberg, T.P.; Caimano, M.J.; Hagadorn, J.I.; Bennett, E.M.; Maas, K.; Brownell, E.A.; Matson, A.P. Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis. J. Matern. Fetal Neonatal Med. 2020, 33, 349–358. [Google Scholar] [CrossRef] [PubMed]
- Nielsen, S.D.; Beverly, R.L.; Underwood, M.A.; Dallas, D.C. Differences and similarities in the peptide profile of preterm and term mother’s milk, and preterm and term infant gastric samples. Nutrients 2020, 12, 2825. [Google Scholar] [CrossRef] [PubMed]
- Beverly, R.L.; Huston, R.K.; Markell, A.M.; McCulley, E.A.; Martin, R.L.; Dallas, D.C. Differences in human milk peptide release along the gastrointestinal tract between preterm and term infants. Clin. Nutr. 2021, 40, 1214–1223. [Google Scholar] [CrossRef] [PubMed]
- Beverly, R.L.; Woonnimani, P.; Scottoline, B.P.; Lueangsakulthai, J.; Dallas, D.C. Peptides from the intestinal tract of breast milk-fed infants have antimicrobial and bifidogenic activity. Int. J. Mol. Sci. 2021, 22, 2377. [Google Scholar] [CrossRef]
- Beverly, R.L.; Huston, R.K.; Markell, A.M.; McCulley, E.A.; Martin, R.L.; Dallas, D.C. Milk peptides survive in vivo gastrointestinal digestion and are excreted in the stool of infants. J. Nutr. 2020, 150, 712–721. [Google Scholar] [CrossRef] [PubMed]
- Lyu, Y.; Chen, Y. Digested human colostrum reduces interleukin-8 production in induced human intestinal epithelial cells. Nutrients 2022, 14, 2787. [Google Scholar] [CrossRef]
- Hornik, C.P.; Fort, P.; Clark, R.H.; Watt, K.; Benjamin, D.K., Jr.; Smith, P.B.; Manzoni, P.; Jacqz-Aigrain, E.; Kaguelidou, F.; Cohen-Wolkowiez, M. Early and late onset sepsis in very-low-birth-weight infants from a large group of neonatal intensive care units. Early Hum. Dev. 2012, 88 (Suppl. S2), S69–S74. [Google Scholar] [CrossRef] [PubMed]
- Friel, J.K.; Diehl-Jones, W.L.; Suh, M.; Tsopmo, A.; Shirwadkar, V.P. Impact of iron and vitamin C-containing supplements on preterm human milk: In vitro. Free Radic. Biol. Med. 2007, 42, 1591–1598. [Google Scholar] [CrossRef] [PubMed]
- Bhadra, P.; Yan, J.; Li, J.; Fong, S.; Siu, S.W. AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest. Sci. Rep. 2018, 8, 1697. [Google Scholar] [CrossRef] [PubMed]
- Tripathi, V.; Tripathi, P. Detecting antimicrobial peptides by exploring the mutual information of their sequences. J. Biomol. Struct. Dyn. 2020, 38, 5037–5043. [Google Scholar] [CrossRef] [PubMed]
- Fleisch, F.; Zimmermann-Baer, U.; Zbinden, R.; Bischoff, G.; Arlettaz, R.; Waldvogel, K.; Nadal, D.; Ruef, C. Three consecutive outbreaks of Serratia marcescens in a neonatal intensive care unit. Clin. Infect Dis. 2002, 34, 767–773. [Google Scholar] [CrossRef] [PubMed]
- Hunter, C.J.; Upperman, J.S.; Ford, H.R.; Camerini, V. Understanding the susceptibility of the premature infant to necrotizing enterocolitis (NEC). Pediatr. Res. 2008, 63, 117–123. [Google Scholar] [CrossRef] [PubMed]
- Moles, L.; Gómez, M.; Moroder, E.; Jiménez, E.; Escuder, D.; Bustos, G.; Melgar, A.; Villa, J.; Del Campo, R.; Chaves, F.; et al. Serratia marcescens colonization in preterm neonates during their neonatal intensive care unit stay. Antimicrob. Resist Infect Control. 2019, 8, 135. [Google Scholar] [CrossRef]
- Garg, P.M.; Paschal, J.L.; Ansari, M.A.Y.; Block, D.; Inagaki, K.; Weitkamp, J.H. Clinical impact of NEC-associated sepsis on outcomes in preterm infants. Pediatr. Res. 2022, 92, 1705–1715. [Google Scholar] [CrossRef] [PubMed]
- Wiegand, I.; Hilpert, K.; Hancock, R.E. Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat. Protoc. 2008, 3, 163–175. [Google Scholar] [CrossRef]
- Belanger, C.R.; Hancock, R.E.W. Testing physiologically relevant conditions in minimal inhibitory concentration assays. Nat. Protoc. 2021, 16, 3761–3774. [Google Scholar] [CrossRef]
- Babicki, S.; Arndt, D.; Marcu, A.; Liang, Y.; Grant, J.R.; Maciejewski, A.; Wishart, D.S. Heatmapper: Web-enabled heat mapping for all. Nucleic Acids Res. 2016, 44, W147–W153. [Google Scholar] [CrossRef] [PubMed]
- Heegaard, C.W.; Larsen, L.B.; Rasmussen, L.K.; Højberg, K.E.; Petersen, T.E.; Andreasen, P.A. Plasminogen activation system in human milk. J. Pediatr. Gastroenterol. Nutr. 1997, 25, 159–166. [Google Scholar] [CrossRef]
- Liepke, C.; Adermann, K.; Raida, M.; Mägert, H.J.; Forssmann, W.G.; Zucht, H.D. Human milk provides peptides highly stimulating the growth of bifidobacteria. Eur. J. Biochem. 2002, 269, 712–718. [Google Scholar] [CrossRef]
- He, Y.; Liu, S.; Leone, S.; Newburg, D.S. Human colostrum oligosaccharides modulate major immunologic pathways of immature human intestine. Mucosal Immunol. 2014, 7, 1326–1339. [Google Scholar] [CrossRef] [PubMed]
- Ackerman, D.L.; Doster, R.S.; Weitkamp, J.H.; Aronoff, D.M.; Gaddy, J.A.; Townsend, S.D. Human milk oligosaccharides exhibit antimicrobial and antibiofilm properties against group B Streptococcus. ACS Infect Dis. 2017, 3, 595–605. [Google Scholar] [CrossRef]
- Thai, J.D.; Gregory, K.E. Bioactive factors in human breast milk attenuate intestinal inflammation during early life. Nutrients 2020, 12, 581. [Google Scholar] [CrossRef]
- Moore, R.E.; Townsend, S.D.; Gaddy, J.A. The diverse antimicrobial activities of human milk oligosaccharides against group B Streptococcus. ChemBioChem 2022, 23, e202100423. [Google Scholar] [CrossRef] [PubMed]
- Spicer, S.K.; Gaddy, J.A.; Townsend, S.D. Recent advances on human milk oligosaccharide antimicrobial activity. Curr. Opin. Chem. Biol. 2022, 71, 102202. [Google Scholar] [CrossRef]
- Mantis, N.J.; Rol, N.; Corthésy, B. Secretory IgA’s complex roles in immunity and mucosal homeostasis in the gut. Mucosal Immunol. 2011, 4, 603–611. [Google Scholar] [CrossRef]
- Chatterton, D.E.; Nguyen, D.N.; Bering, S.B.; Sangild, P.T. Anti-inflammatory mechanisms of bioactive milk proteins in the intestine of newborns. Int. J. Biochem. Cell Biol. 2013, 45, 1730–1747. [Google Scholar] [CrossRef]
- Johnson-Hence, C.B.; Gopalakrishna, K.P.; Bodkin, D.; Coffey, K.E.; Burr, A.H.P.; Rahman, S.; Rai, A.T.; Abbott, D.A.; Sosa, Y.A.; Tometich, J.T.; et al. Stability and heterogeneity in the antimicrobiota reactivity of human milk-derived immunoglobulin A. J. Exp. Med. 2023, 220, e20220839. [Google Scholar] [CrossRef] [PubMed]
Counts of Peptides Identified by MBPDB Search | Undigested | Digested |
---|---|---|
Total | 152 | 64 |
ACE-inhibitory | 35 | 43 |
Anticancer | - | 2 |
Antimicrobial | 45 | 1 |
Antioxidant | 1 | 4 |
DPP-IV Inhibitory | - | 1 |
Immunomodulatory | 19 | 2 |
Increase cellular growth | 52 | 9 |
Opioid | - | 2 |
C. freundii | E. coli | K. aerogenes | S. marcescens | |||
---|---|---|---|---|---|---|
Peptide ID | Sequence | Predicted Probability of AMPs | MIC | MIC | MIC | MIC |
αS1-casein [157–163] | QYVPFPP | 0.67 | >2500 | >2500 | 2500 | >2500 |
αS1-casein [157–165] | QYVPFPPFS | 0.73 | 2500 | >2500 | 2500 | >2500 |
β-casein [153–159] | VPQPIPQ | 0.61 | 2500 | >2500 | 2500 | >2500 |
plasminogen [591–597] | SWPWQVS | 0.55 | 2500 | >2500 | 2500 | >2500 |
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Lyu, Y.; Kim, B.J.; Patel, J.S.; Dallas, D.C.; Chen, Y. Human Milk Protein-Derived Bioactive Peptides from In Vitro-Digested Colostrum Exert Antimicrobial Activities against Common Neonatal Pathogens. Nutrients 2024, 16, 2040. https://doi.org/10.3390/nu16132040
Lyu Y, Kim BJ, Patel JS, Dallas DC, Chen Y. Human Milk Protein-Derived Bioactive Peptides from In Vitro-Digested Colostrum Exert Antimicrobial Activities against Common Neonatal Pathogens. Nutrients. 2024; 16(13):2040. https://doi.org/10.3390/nu16132040
Chicago/Turabian StyleLyu, Yang, Bum Jin Kim, Jagdish Suresh Patel, David C. Dallas, and Yimin Chen. 2024. "Human Milk Protein-Derived Bioactive Peptides from In Vitro-Digested Colostrum Exert Antimicrobial Activities against Common Neonatal Pathogens" Nutrients 16, no. 13: 2040. https://doi.org/10.3390/nu16132040