Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis

Scientific Reports

Volumn 7, Issue 1, 2017, Pages

  Braun, Tzipi ^a   Di Segni, Ayelet ^a   Benshoshan, Marina ^a   Asaf, Roy ^a   Squires, James E ^b   Farage Barhom, Sarit ^a   Glick Saar, Efrat ^a   Cesarkas, Karen ^a   Smollan, Gill ^a   Weiss, Batia ^a,c   Amit, Sharon ^a   Keller, Nathan ^a,c   Haberman, Yael ^a,d  

^a SHEBA MEDICAL CENTER   (Israel)

^b CHILDREN S HOSPITAL OF PITTSBURGH   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

^d CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ADOLESCENT; ADULT; AGED; BACTERIUM; CHEMISTRY; CHILD; CLASSIFICATION; CLUSTER ANALYSIS; DIARRHEA; DNA SEQUENCE; DYSBIOSIS; FECES; FEMALE; GENETICS; HOSPITALIZATION; HUMAN; MALE; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; PHYLOGENY; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; BACTERIA; CHILD; CLUSTER ANALYSIS; DIARRHEA; DNA, BACTERIAL; DNA, RIBOSOMAL; DYSBIOSIS; FECES; FEMALE; HOSPITALIZATION; HUMANS; MALE; MICROBIOTA; MIDDLE AGED; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 85018370609     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-017-01217-1     Document Type: Article

References (44)

1. Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222-227, doi:10.1038/nature11053 (2012).
2. Rodriguez, J. M. et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis 26, 26050, doi:10.3402/mehd.v26.26050 (2015).
3. De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 107, 14691-14696, doi:10.1073/pnas.1005963107 (2010).
4. Turnbaugh, P. J. et al. An obesity-Associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031, doi:10.1038/nature05414 (2006).
5. McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME journal 6, 610-618, doi:10.1038/ismej.2011.139 (2012).
6. Yassour, M. et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 8, 343ra381, doi:10.1126/scitranslmed.aad0917 (2016).
7. Magill, S. S. et al. Multistate point-prevalence survey of health care-Associated infections. N Engl J Med 370, 1198-1208, doi:10.1056/NEJMoa1306801 (2014).
8. Bartosch, S., Fite, A., Macfarlane, G. T. & McMurdo, M. E. Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-Time PCR and effects of antibiotic treatment on the fecal microbiota. Appl Environ Microbiol 70, 3575-3581, doi:10.1128/AEM.70.6.3575-3581.2004 (2004).
9. Youmans, B. P. et al. Characterization of the human gut microbiome during travelers diarrhea. Gut Microbes 6, 110-119, doi:10.10 80/19490976.2015.1019693 (2015).
10. David, L. A. et al. Gut microbial succession follows acute secretory diarrhea in humans. MBio 6, e00381-00315, doi:10.1128/mBio.00381-15 (2015).
11. Koplan, J. P., Fineberg, H. V., Ferraro, M. J. & Rosenberg, M. L. Value of stool cultures. Lancet 2, 413-416 (1980).
12. Platts-Mills, J. A., Liu, J. & Houpt, E. R. New concepts in diagnostics for infectious diarrhea. Mucosal Immunol 6, 876-885, doi:10.1038/mi.2013.50 (2013).
13. Mellmann, A. et al. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6, e22751, doi:10.1371/journal.pone.0022751 (2011).
14. Pop, M. et al. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biol 15, R76, doi:10.1186/gb-2014-15-6-r76 (2014).
15. Bruzzese, E. et al. Randomised clinical trial: A Lactobacillus GG and micronutrient-containing mixture is effective in reducing nosocomial infections in children, vs. placebo. Alimentary pharmacology & therapeutics 44, 568-575, doi:10.1111/apt.13740 (2016).
16. Zeevi, D. et al. Personalized Nutrition by Prediction of Glycemic Responses. Cell 163, 1079-1094, doi:10.1016/j.cell.2015.11.001 (2015).
17. Bokulich, N. A. et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 8, 343ra382, doi:10.1126/scitranslmed.aad7121 (2016).
18. Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome biology 13, R79, doi:10.1186/gb-2012-13-9-r79 (2012).
19. Haberman, Y. et al. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest 124, 3617-3633, doi:10.1172/JCI75436 (2014).
20. Gevers, D. et al. The treatment-naive microbiome in new-onset Crohns disease. Cell Host Microbe 15, 382-392, doi:10.1016/j. chom.2014.02.005 (2014).
21. Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: An effective distance metric for microbial community comparison. ISME J 5, 169-172, doi:10.1038/ismej.2010.133 (2011).
22. Mariat, D. et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9, 123, doi:10.1186/1471-2180-9-123 (2009).
23. Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022-1023, doi:10.1038/4441022a (2006).
24. Tilg, H. & Kaser, A. Gut microbiome, obesity, and metabolic dysfunction. J Clin Invest 121, 2126-2132, doi:10.1172/JCI58109 (2011).
25. Visca, P., Seifert, H. & Towner, K. J. Acinetobacter infection-An emerging threat to human health. IUBMB life 63, 1048-1054, doi:10.1002/iub.534 (2011).
26. Finegold, S., Summanen, P., Hunt Gerardo, S. & Baron, E. Clinical importance of Bilophila wadsworthia. European journal of clinical microbiology & infectious diseases: official publication of the European Society of Clinical Microbiology 11, 1058-1063 (1992).
27. Srinivasan, R. et al. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PloS one 10, e0117617, doi:10.1371/journal.pone.0117617 (2015).
28. Hiergeist, A., Glasner, J., Reischl, U. & Gessner, A. Analyses of Intestinal Microbiota: Culture versus Sequencing. ILAR journal 56, 228-240, doi:10.1093/ilar/ilv017 (2015).
29. Didelot, X., Bowden, R., Wilson, D. J., Peto, T. E. & Crook, D. W. Transforming clinical microbiology with bacterial genome sequencing. Nature reviews. Genetics 13, 601-612, doi:10.1038/nrg3226 (2012).
30. Salipante, S. J. et al. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PloS one 8, e65226, doi:10.1371/journal.pone.0065226 (2013).
31. Jeffery, I. B. et al. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut 61, 997-1006, doi:10.1136/gutjnl-2011-301501 (2012).
32. Krogius-Kurikka, L. et al. Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC gastroenterology 9, 95, doi:10.1186/1471-230X-9-95 (2009).
33. Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences of the United States of America 104, 13780-13785, doi:10.1073/pnas.0706625104 (2007).
34. Langdon, A., Crook, N. & Dantas, G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome medicine 8, 39, doi:10.1186/s13073-016-0294-z (2016).
35. Azad, M. B. et al. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 185, 385-394, doi:10.1503/cmaj.121189 (2013).
36. Huda, M. N. et al. Stool microbiota and vaccine responses of infants. Pediatrics 134, e362-372, doi:10.1542/peds.2013-3937 (2014).
37. Penders, J. et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118, 511-521, doi:10.1542/peds.2005-2824 (2006).
38. Fanaro, S., Chierici, R., Guerrini, P. & Vigi, V. Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl 91, 48-55 (2003).
39. Caporaso, J. G. et al. Ultra-high-Throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal 6, 1621-1624, doi:10.1038/ismej.2012.8 (2012).
40. Flores, G. E., Henley, J. B. & Fierer, N. A direct PCR approach to accelerate analyses of human-Associated microbial communities. PLoS One 7, e44563, doi:10.1371/journal.pone.0044563 (2012).
41. Flores, G. E. et al. Temporal variability is a personalized feature of the human microbiome. Genome biology 15, 531, doi:10.1186/s13059-014-0531-y (2014).
42. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461, doi:10.1093/bioinformatics/btq461 (2010).
43. Faith, D. P. Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1-10, doi:10.1016/0006-3207(92)91201-3 (1992).
44. Lozupone, C. & Knight, R. UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 8228-8235, doi:10.1128/AEM.71.12.8228-8235.2005 (2005).