REFERENCES

1. Chin VK, Yong VC, Chong PP, Amin Nordin S, Basir R, Abdullah M. Mycobiome in the gut: a multiperspective review. Mediators Inflamm 2020;2020:9560684.

2. Manor O, Dai CL, Kornilov SA, et al. Health and disease markers correlate with gut microbiome composition across thousands of people. Nat Commun 2020;11:5206.

3. Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. N Engl J Med 2016;375:2369-79.

4. Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol 2021;19:55-71.

5. Pfeiffer JK, Virgin HW. Viral immunity. Transkingdom control of viral infection and immunity in the mammalian intestine. Science 2016;351:aad5872.

6. Schei K, Avershina E, Øien T, et al. Early gut mycobiota and mother-offspring transfer. Microbiome 2017;5:107.

7. Bliss JM, Basavegowda KP, Watson WJ, Sheikh AU, Ryan RM. Vertical and horizontal transmission of Candida albicans in very low birth weight infants using DNA fingerprinting techniques. Pediatr Infect Dis J 2008;27:231-5.

8. Ward TL, Dominguez-Bello MG, Heisel T, Al-Ghalith G, Knights D, Gale CA. Development of the human mycobiome over the first month of life and across body sites. mSystems 2018;3:e00140-17.

9. Ward TL, Knights D, Gale CA. Infant fungal communities: current knowledge and research opportunities. BMC Med 2017;15:30.

10. Strati F, Di Paola M, Stefanini I, et al. Age and gender affect the composition of fungal population of the human gastrointestinal tract. Front Microbiol 2016;7:1227.

11. James SA, Phillips S, Telatin A, et al. Preterm infants harbour a rapidly changing mycobiota that includes Candida pathobionts. J Fungi (Basel) 2020;6:273.

12. Mason KL, Erb Downward JR, Mason KD, et al. Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infect Immun 2012;80:3371-80.

13. Filyk HA, Osborne LC. The multibiome: the intestinal ecosystem’s influence on immune homeostasis, health, and disease. EBioMedicine 2016;13:46-54.

14. LaTuga MS, Ellis JC, Cotton CM, et al. Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants. PLoS One 2011;6:e27858.

15. Underhill DM, Iliev ID. The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol 2014;14:405-16.

16. Moré MI, Swidsinski A. Saccharomyces boulardii CNCM I-745 supports regeneration of the intestinal microbiota after diarrheic dysbiosis - a review. Clin Exp Gastroenterol 2015;8:237-55.

17. Zanello G, Meurens F, Berri M, Salmon H. Saccharomyces boulardii effects on gastrointestinal diseases. Curr Issues Mol Biol 2009;11:47-58.

18. Greenberg RG, Benjamin DK Jr. Neonatal candidiasis: diagnosis, prevention, and treatment. J Infect 2014;69 Suppl 1:S19-22.

19. Benjamin DK Jr, Stoll BJ, Fanaroff AA, et al. National Institute of Child Health and Human Development Neonatal Research Network. Neonatal candidiasis among extremely low birth weight infants: risk factors, mortality rates, and neurodevelopmental outcomes at 18 to 22 months. Pediatrics 2006;117:84-92.

20. Henderickx JGE, Zwittink RD, Renes IB, et al. Maturation of the preterm gastrointestinal tract can be defined by host and microbial markers for digestion and barrier defense. Sci Rep 2021;11:12808.

21. Zwittink RD, van Zoeren-Grobben D, Martin R, et al. Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants. Mol Cell Proteomics 2017;16:1610-20.

22. Zwittink RD, van Zoeren-Grobben D, Renes IB, et al. Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment. BMC Pediatr 2020;20:195.

23. Zwittink RD, Renes IB, van Lingen RA, et al. Association between duration of intravenous antibiotic administration and early-life microbiota development in late-preterm infants. Eur J Clin Microbiol Infect Dis 2018;37:475-83.

24. Stecher G, Tamura K, Kumar S. Molecular evolutionary genetics analysis (MEGA) for macOS. Mol Biol Evol 2020;37:1237-9.

25. Rivers AR. Q2-ITSxpress: a tutorial on a QIIME 2 plugin to trim ITS sequences. Available from: https://forum.qiime2.org/t/q2-itsxpress-a-tutorial-on-a-qiime-2-plugin-to-trim-its-sequences/5780 [Last accessed on 18 Jan 2022].

26. Rivers AR, Weber KC, Gardner TG, Liu S, Armstrong SD. ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Res 2018;7:1418.

27. Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett 2009;296:97-101.

28. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 2016;13:581-3.

29. Abarenkov K, Zirk A, Piirmann T, et al. UNITE QIIME release for eukaryotes. 2021; doi: 10.15156/BIO/1264819.

30. R Core Team. R: a language and environment for statistical computing. Available from: https://www.r-project.org/ [Last accessed on 18 Jan 2022].

31. Bisanz JE. qiime2R: importing QIIME2 artifacts and associated data into R sessions. Available from: https://github.com/jbisanz/qiime2R [Last accessed on 18 Jan 2022].

32. Lahti L, Shetty S. microbiome R package. Bioconductor 2017; doi: 10.18129/B9.bioc.microbiome.

33. Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2016.

34. Kassambara A. ggpubr: “ggplot2” based publication ready plots. Available from: https://rpkgs.datanovia.com/ggpubr/ [Last accessed on 18 Jan 2022].

35. Revelle W. psych: procedures for psychological, psychometric, and personality research. Available from: https://cran.r-project.org/package=psych [Last accessed on 18 Jan 2022]

36. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 2013;8:e61217.

37. Galili T. dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 2015;31:3718-20.

38. Kembel SW, Cowan PD, Helmus MR, et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 2010;26:1463-4.

39. Oksanen J, Guillaume Blanchet F, Friendly M, et al. vegan: community ecology package. Available from: https://cran.r-project.org/package=vegan [Last accessed on 18 Jan 2022].

40. Aitchison J, Barceló-Vidal C, Martín-Fernández JA, Pawlowsky-Glahn V. Logratio analysis and compositional distance. Math Geol 2000;32:271-5.

41. Quinn TP, Erb I, Richardson MF, Crowley TM. Understanding sequencing data as compositions: an outlook and review. Bioinformatics 2018;34:2870-8.

42. Rrumen. Available from: https://github.com/seashore001x/Rrumen/blob/master/phyloseq2lefse.R [Last accessed on 18 Jan 2022].

43. Pandey PK, Siddharth J, Verma P, Bavdekar A, Patole MS, Shouche YS. Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers. J Biosci 2012;37:221-6.

44. Greenberg JA, Bell SJ, Van Ausdal W. Omega-3 fatty acid supplementation during pregnancy. Rev Obstet Gynecol 2008;1:162-9.

45. von Schacky C. Omega-3 fatty acids in pregnancy-the case for a target Omega-3 index. Nutrients 2020;12:898.

46. Richard ML, Sokol H. The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 2019;16:331-45.

47. Cotten CM, McDonald S, Stoll B, Goldberg RN, Poole K, Benjamin DK Jr. National Institute for Child Health and Human Development Neonatal Research Network. The association of third-generation cephalosporin use and invasive candidiasis in extremely low birth-weight infants. Pediatrics 2006;118:717-22.

48. Saiman L, Ludington E, Pfaller M, et al. Risk factors for candidemia in Neonatal Intensive Care Unit patients. The National Epidemiology of Mycosis Survey study group. Pediatr Infect Dis J 2000;19:319-24.

49. Barton M, O'Brien K, Robinson JL, et al. Invasive candidiasis in low birth weight preterm infants: risk factors, clinical course and outcome in a prospective multicenter study of cases and their matched controls. BMC Infect Dis 2014;14:327.

50. Kelly MS, Benjamin DK Jr, Smith PB. The epidemiology and diagnosis of invasive candidiasis among premature infants. Clin Perinatol 2015;42:105-17, viii.

51. Ali GY, Algohary EH, Rashed KA, Almoghanum M, Khalifa AA. Prevalence of Candida colonization in preterm newborns and VLBW in neonatal intensive care unit: role of maternal colonization as a risk factor in transmission of disease. J Matern Fetal Neonatal Med 2012;25:789-95.

52. Kaufman D. “Getting to Zero”: preventing invasive Candida infections and eliminating infection-related mortality and morbidity in extremely preterm infants. Early Human Development 2012;88:S45-9.

53. Pappas PG, Lionakis MS, Arendrup MC, Ostrosky-Zeichner L, Kullberg BJ. Invasive candidiasis. Nat Rev Dis Primers 2018;4:18026.

54. Çerikçioǧlu N, Ilki A, Bilgen H, Özek E, Metin F, Kalaça S. The relationships between candidemia and candidal colonization and virulence factors of the colonizing strains in preterm infants. Turk J Pediatr 2004;46:245-50.

55. Coates EW, Karlowicz MG, Croitoru DP, Buescher ES. Distinctive distribution of pathogens associated with peritonitis in neonates with focal intestinal perforation compared with necrotizing enterocolitis. Pediatrics 2005;116:e241-6.

56. Parra-Herran CE, Pelaez L, Sola JE, Urbiztondo AK, Rodriguez MM. Intestinal candidiasis: an uncommon cause of necrotizing enterocolitis (NEC) in neonates. Fetal Pediatr Pathol 2010;29:172-80.

57. Tso GHW, Reales-Calderon JA, Tan ASM, et al. Experimental evolution of a fungal pathogen into a gut symbiont. Science 2018;362:589-95.

58. Heisel T, Nyaribo L, Sadowsky MJ, Gale CA. Breastmilk and NICU surfaces are potential sources of fungi for infant mycobiomes. Fungal Genet Biol 2019;128:29-35.

59. Boix-Amorós A, Puente-Sánchez F, du Toit E, et al. Mycobiome profiles in breast milk from healthy women depend on mode of delivery, geographic location, and interaction with bacteria. Appl Environ Microbiol 2019;85:e02994-18.

60. Findley K, Oh J, Yang J, et al. NIH Intramural Sequencing Center Comparative Sequencing Program. Topographic diversity of fungal and bacterial communities in human skin. Nature 2013;498:367-70.

61. Nagata R, Nagano H, Ogishima D, Nakamura Y, Hiruma M, Sugita T. Transmission of the major skin microbiota, Malassezia, from mother to neonate. Pediatr Int 2012;54:350-5.

62. Dominguez-Bello MG, Costello EK, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010;107:11971-5.

63. Qin J, Li R, Raes J, et al. MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.

64. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 2016;14:e1002533.

65. Tiew PY, Mac Aogain M, Ali NABM, et al. The Mycobiome in health and disease: emerging concepts, methodologies and challenges. Mycopathologia 2020;185:207-31.

66. Mac Aogáin M, Chaturvedi V, Chotirmall SH. MycopathologiaGENOMES: the new ‘home’ for the publication of fungal genomes. Mycopathologia 2019;184:551-4.

67. Gabaldón T. Consortium OPATHY. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019;43:517-47.

Microbiome Research Reports
ISSN 2771-5965 (Online)

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/