Abdulkadir B, Nelson A, Skeath T, et al. Routine use of probiotics in preterm infants: longitudinal impact on the microbiome and metabolome. Neonatology. 2016;109(4):239–47.

Article  CAS  PubMed  Google Scholar 

Alcon-Giner C, Dalby MJ, Caim S, et al. Microbiota supplementation with bifidobacterium and lactobacillus modifies the preterm infant gut microbiota and metabolome: an observational study. Cell Rep Med. 2020;1(5): 100077.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alexander VN, Northrup V, Bizzarro MJ. Antibiotic exposure in the newborn intensive care unit and the risk of necrotizing enterocolitis. J Pediatr. 2011;159(3):392–7.

Article  PubMed  PubMed Central  Google Scholar 

Araújo BC, Guimarães H. Risk factors for neonatal sepsis: an overview. J Pediatr Neonatal Individ Med (JPNIM). 2020;9(2):e090206–e090206.

Google Scholar 

Arboleya S, Sánchez B, Milani C, et al. Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics. J Pediatr. 2015;166(3):538–44.

Article  CAS  PubMed  Google Scholar 

Behrman RE, Butler AS. Preterm birth: causes, consequences, and prevention. Washington, DC: The National Academies Press; 2007. https://doi.org/10.17226/11622.

Book  Google Scholar 

Bender JM, Li F, Purswani H, et al. Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome. J Maternal Fetal Neonatal Med. 2021;34(20):3335–43.

Article  CAS  Google Scholar 

Bhatta DR, Hosuru Subramanya S, Hamal D, et al. Bacterial contamination of neonatal intensive care units: How safe are the neonates? Antimicrob Resist Infect Control. 2021;10(1):26. https://doi.org/10.1186/s13756-021-00901-2.

Article  PubMed  PubMed Central  Google Scholar 

Bolyen E, Rideout JR, Dillon MR, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boutin RC, Petersen C, Woodward SE, et al. Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life. eLife. 2021. https://doi.org/10.7554/elife.67740.

Article  PubMed  PubMed Central  Google Scholar 

Brooks ME, Kristensen K, Van Benthem KJ, et al. glmm TMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R J. 2017;9(2):378–400.

Article  Google Scholar 

Brown HK, Speechley KN, Macnab J, et al. Neonatal morbidity associated with late preterm and early term birth: the roles of gestational age and biological determinants of preterm birth. Int J Epidemiol. 2014;43(3):802–14.

Article  PubMed  Google Scholar 

Bryda EC. The mighty mouse: the impact of rodents on advances in biomedical research. Mo Med. 2013;110(3):207.

PubMed  PubMed Central  Google Scholar 

Bührer C, Fischer HS, Wellmann S. Nutritional interventions to reduce rates of infection, necrotizing enterocolitis and mortality in very preterm infants. Pediatr Res. 2020;87(2):371–7.

Article  PubMed  Google Scholar 

Callahan BJ, McMurdie PJ, Rosen MJ, et al. Dada2: High-resolution sample inference from illumina amplicon data. Nat Methods. 2016;13(7):581–3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chang HY, Chen JH, Chang JH, et al. Multiple strains probiotics appear to be the most effective probiotics in the prevention of necrotizing enterocolitis and mortality: an updated meta-analysis. PLoS ONE. 2017;12(2): e0171579.

Article  PubMed  PubMed Central  Google Scholar 

Chen J, Li H, Hird SM, et al. Sex differences in gut microbial development of preterm infant twins in early life: a longitudinal analysis. Front Cell Infect Microbiol. 2021. https://doi.org/10.3389/fcimb.2021.671074.

Article  PubMed  PubMed Central  Google Scholar 

Chen S, Zhou Y, Chen Y, et al. fastp: an ultra-fast all-in-one fastq preprocessor. Bioinformatics. 2018;34(17):i884–90.

Article  PubMed  PubMed Central  Google Scholar 

Chernikova DA, Madan JC, Housman ML, et al. The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth. Pediatr Res. 2018;84(1):71–9.

Article  PubMed  PubMed Central  Google Scholar 

Chin VK, Yong VC, Chong PP, et al. Mycobiome in the gut: a multiperspective review. Mediat Inflamm. 2020. https://doi.org/10.1155/2020/9560684.

Article  Google Scholar 

Cotten CM, Taylor S, Stoll B, et al. Prolonged duration of initial empirical antibiotic treatment is associated with increased rates of necrotizing enterocolitis and death for extremely low birth weight infants. Pediatrics. 2009;123(1):58–66.

Article  PubMed  Google Scholar 

Couto RC, Carvalho EA, Pedrosa TM, et al. A 10-year prospective surveillance of nosocomial infections in neonatal intensive care units. Am J Infect Control. 2007;35(3):183–9. https://doi.org/10.1016/j.ajic.2006.06.013.

Article  PubMed  Google Scholar 

Denkel LA, Schwab F, Garten L, et al. Protective effect of dual-strain probiotics in preterm infants: a multi-center time series analysis. PLoS ONE. 2016;11(6): e0158136.

Article  PubMed  PubMed Central  Google Scholar 

Dixon P. Vegan, a package of R functions for community ecology. J veg Sci. 2003;14(6):927–30.

Article  Google Scholar 

Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 2016;14(1):20–32.

Article  CAS  PubMed  Google Scholar 

van Duin D, Paterson DL. Multidrug-resistant bacteria in the community. Infect Dis Clin N Am. 2016;30(2):377–90. https://doi.org/10.1016/j.idc.2016.02.004.

Article  Google Scholar 

Esaiassen E, Hjerde E, Cavanagh JP, et al. Effects of probiotic supplementation on the gut microbiota and antibiotic resistome development in preterm infants. Front Pediatr. 2018;6:347.

Article  PubMed  PubMed Central  Google Scholar 

Fouhy F, Guinane CM, Hussey S, et al. High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin. Antimicrob Agents Chemother. 2012;56(11):5811–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

García-Basteiro AL, Quintó L, Macete E, et al. Infant mortality and morbidity associated with preterm and small-for-gestational-age births in southern mozambique: a retrospective cohort study. PLoS ONE. 2017;12(2):1–14. https://doi.org/10.1371/journal.pone.0172533.

Article  CAS  Google Scholar 

Ge X, Ding C, Zhao W, et al. Antibiotics-induced depletion of mice microbiota induces changes in host serotonin biosynthesis and intestinal motility. J Transl Med. 2017;15(1):1–9.

Article  Google Scholar 

Gibson MK, Wang B, Ahmadi S, et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat Microbiol. 2016;1(4):1–10.

Article  Google Scholar 

Godeluck A, Gérardin P, Lenclume V, et al. Mortality and severe morbidity of very preterm infants: comparison of two French cohort studies. BMC Pediatr. 2019;19:1–9.

Article  Google Scholar 

Gupta SK, Padmanabhan BR, Diene SM, et al. Arg-annot, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrobial agents and chemotherapy. 2014;58(1):212–20.

Article  PubMed  PubMed Central  Google Scholar 

Gustavsson L, Lindquist S, Elfvin A, et al. Reduced antibiotic use in extremely preterm infants with an antimicrobial stewardship intervention. BMJ Paediatr Open. 2020;4(1): e000872. https://doi.org/10.1136/bmjpo-2020-000872.

Article  PubMed  PubMed Central  Google Scholar 

Gweon HS, Oliver A, Taylor J, et al. Pipits: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the i llumina sequencing platform. Methods Ecol Evol. 2015;6(8):973–80.

Article  PubMed  PubMed Central  Google Scholar 

Heisel T, Podgorski H, Staley CM, et al. Complementary amplicon-based genomic approaches for the study of fungal communities in humans. PLoS ONE. 2015;10(2): e0116705.

Article  PubMed  PubMed Central  Google Scholar 

Henderickx JGE, Zwittink RD, van Lingen RA, et al. The preterm gut microbiota: an inconspicuous challenge in nutritional neonatal care. Front Cell Infect Microbiol. 2019. https://doi.org/10.3389/fcimb.2019.00085.

Article  PubMed  PubMed Central  Google Scholar 

Inouye M, Dashnow H, Raven LA, et al. Srst2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6(11):1–16.

Article  Google Scholar 

James SA, Phillips S, Telatin A, et al. Preterm infants harbour a rapidly changing mycobiota that includes candida pathobionts. J Fungi. 2020;6(4):273.

Article  Google Scholar 

Ji X, Su L, Zhang P, et al. Lentinan improves intestinal inflammation and gut dysbiosis in antibiotics-induced mice. Sci Rep. 2022;12(1):19609.

Article