Network analysis suggests a potentially 'evil' alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Ma, Zhanshan ^a   Guan, Qiong ^a   Ye, Chengxi ^a,b   Zhang, Chengchen ^c   Foster, James A ^d   Forney, Larry J ^d  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b University of Maryland ^*  (United States)

^c NewYork Presbyterian Hospital   (United States)

^d UNIVERSITY OF IDAHO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

BACTERIUM; BREAST MILK; CLASSIFICATION; FOOD CONTROL; GENETICS; HUMAN; MICROBIOLOGY; MICROFLORA; PHYLOGENY; THEORETICAL MODEL;

BACTERIA; FOOD MICROBIOLOGY; HUMANS; MICROBIOTA; MILK, HUMAN; MODELS, THEORETICAL; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84953226740     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08275     Document Type: Article

References (46)

1. Hunt, K. M. et al. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS ONE 6, e21313 (2011).
2. Fernández, L. et al. The human milk microbiota: origin and potential roles in health and disease. Pharmacol. Res. 69, 1-10 (2013).
3. Gregory, K. E. & Walker, W. A. Immunologic Factors in Human Milk and Disease Prevention in the Preterm Infant. Curr Pediatr Rep 1, 222-228 (2013).
4. Ward, T. L., Hosid, S., Ioshikhes, I. & Altosaar, I. Human milk metagenome: a functional capacity analysis. BMC Microbiol. 13, 116 (2013).
5. Latuga, M. S., Stuebe, A. & Seed, P. C. A review of the source and function of microbiota in breast milk. Semin. Reprod. Med. 32, 68-73 (2014).
6. Heikkilä, M. P. & Saris, P. E. J. Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. J. Appl. Microbiol. 95, 471-478 (2003).
7. Farr, B. M., Salgado, C. D., Karchmer, T. B. & Sherertz, R. J. Can antibioticresistant nosocomial infections be controlled? Lancet Infect Dis 1, 38-45 (2001).
8. Zorgani, A. et al. Detection of pyrogenic toxins of Staphylococcus aureus in sudden infant death syndrome. FEMS Immunol. Med. Microbiol. 25, 103-108 (1999).
9. Blackwell, C. C. et al. Toxigenic bacteria and sudden infant death syndrome (SIDS): nasopharyngeal flora during the first year of life. FEMS Immunol. Med. Microbiol. 25, 51-58 (1999).
10. Jonsson, S. & Pulkkinen, M. O. Mastitis today: incidence, prevention and treatment. Ann Chir Gynaecol Suppl 208, 84-87 (1994).
11. Semba, R. D. et al. Mastitis and immunological factors in breast milk of lactating women in Malawi. Clin. Diagn. Lab. Immunol. 6, 671-674 (1999).
12. Perez, P. F. et al. Bacterial imprinting of the neonatal immune system: lessons from maternal cells? Pediatrics 119, e724-732 (2007).
13. Martín, R. et al. Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women. Res. Microbiol. 158, 31-37 (2007).
14. Martín, R. 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. 75, 965-969 (2009).
15. Gueimonde, M., Laitinen, K., Salminen, S. & Isolauri, E. Breast milk: a source of bifidobacteria for infant gut development and maturation? Neonatology 92, 64-66 (2007).
16. Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J. & Knight, R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5, 235-237 (2008).
17. Collado, M. C., Delgado, S., Maldonado, A. & Rodríguez, J. M. Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR. Lett. Appl. Microbiol. 48, 523-528 (2009).
18. Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M. & Relman, D. A. The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255-1262 (2012).
19. Zaura, E., Nicu, E. A., Krom, B. P. & Keijser, B. J. F. Acquiring and maintaining a normal oral microbiome: current perspective. Front Cell Infect Microbiol 4, 85 (2014).
20. Jeurink, P. V. et al. Human milk: a source of more life than we imagine. Benef Microbes 4, 17-30 (2013).
21. Matamoros, S., Gras-Leguen, C., Le Vacon, F., Potel, G. & de La Cochetiere, M.-F. Development of intestinal microbiota in infants and its impact on health. Trends Microbiol. 21, 167-173 (2013).
22. González, R. et al. Breast milk and gut microbiota in African mothers and infants from an area of high HIV prevalence. PLoS ONE 8, e80299 (2013).
23. Xuan, C. et al. Microbial dysbiosis is associated with human breast cancer. PLoS ONE 9, e83744 (2014).
24. Guan, Q. & Ma, Z. S. Ecological analysis of the human milk microbiome. Chinese Science Bulletin 59, 2205-2212 (2014).
25. Ma, Z. S., Abdo, Z. & Forney, L. J. Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. Personalized Medicine 8, 681-688 (2011).
26. Ma, Z. S., Geng, J. W., Abdo, Z. & Forney, L. J. [A Bird's Eye View of Microbial Community Dynamics.] Microbial Ecological Theory: Current Perspectives [Ogilvie, L. A. and Hirsch, P. R. (ed.)][pp57-71] (Caister Academic Press London, 2012).
27. Erdos, P. & Rényi, A. On the Evolution of Random Graphs. Publication of the Mathematical Institute of the Hungarian Academy of Sciences 5, 17-61 (1960).
28. Watts, D. J. & Strogatz, S. H. Collective dynamics of 'small-world' networks. Nature 393, 440-442 (1998).
29. Barabasi, A. L. & Albert, R. Emergence of scaling in random networks. Science 286, 509-512 (1999).
30. Foster, J. A., Krone, S. M. & Forney, L. J. Application of ecological network theory to the human microbiome. Interdiscip Perspect Infect Dis 2008, 839501 (2008).
31. Bapteste, E., Bicep, C. & Lopez, P. Evolution of genetic diversity using networks: the human gut microbiome as a case study. Clin. Microbiol. Infect. 18 Suppl 4, 40-43 (2012).
32. Greenblum, S., Turnbaugh, P. J. & Borenstein, E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc. Natl. Acad. Sci. U.S.A. 109, 594-599 (2012).
33. Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).
34. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
35. st, 2009.
36. Kuchaiev, O., Stevanović, A., Hayes, W. & Pržulj, N. Graph Crunch 2: Software tool for network modeling, alignment and clustering. BMC Bioinformatics 12, 24 (2011).
37. Delgado, S., Arroyo, R., Martín, R. & Rodríguez, J. M. PCR-DGGE assessment of the bacterial diversity of breast milk in women with lactational infectiousmastitis. BMC Infect. Dis. 8, 51 (2008).
38. Delgado, S. et al. Staphylococcus epidermidis strains isolated from breast milk of women suffering infectious mastitis: potential virulence traits and resistance to antibiotics. BMC Microbiol. 9, 82 (2009).
39. Arroyo, R. et al. Treatment of infectious mastitis during lactation: antibiotics versus oral administration of Lactobacilli isolated from breast milk. Clin. Infect. Dis. 50, 1551-1558 (2010).
40. Brown, K. H., Black, R. E., Lopez de Romaña, G. & Creed de Kanashiro, H. Infantfeeding practices and their relationship with diarrheal and other diseases in Huascar (Lima), Peru. Pediatrics 83, 31-40 (1989).
41. López-Alarcón, M., Villalpando, S. & Fajardo, A. Breast-feeding lowers the frequency and duration of acute respiratory infection and diarrhea in infants under six months of age. J. Nutr. 127, 436-443 (1997).
42. Osterman, K. L. & Rahm, V. A. Lactation mastitis: bacterial cultivation of breast milk, symptoms, treatment, and outcome. J Hum Lact 16, 297-302 (2000).
43. Fetherston, C. Mastitis in lactating women: physiology or pathology? Breastfeed Rev 9, 5-12 (2001).
44. Barbosa-Cesnik, C., Schwartz, K. & Foxman, B. Lactation mastitis. JAMA 289, 1609-1612 (2003).
45. Foxman, B., D'Arcy, H., Gillespie, B., Bobo, J. K. & Schwartz, K. Lactation mastitis: occurrence and medical management among 946 breastfeeding women in the United States. Am. J. Epidemiol. 155, 103-114 (2002).
46. Urbaniak, C. et al. Microbiota of human breast tissue. Appl. Environ. Microbiol. 80, 3007-3014 (2014).