prematurity and nutrition on the developing gut microbiome and preterm infant growth. Microbiome,
2017. 5(1): p. 158. 99 Zwittink, R.D., et al., Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants. Mol Cell
Proteomics, 2017. 16(9): p. 1610-1620.
162 Van Der Zwet, W.C., et al., Nosocomial spread of
a Staphylococcus capitis strain with heteroresistance to vancomycin in a neonatal intensive care unit. J Clin
Microbiol, 2002. 40(7): p. 2520-5.
163 Isaac, S., et al., Short- and
long-term effects of oral vancomycin on the human intestinal microbiota.
J Antimicrob Chemother, 2017. 72(1): p. 128-136.
164 Korpela, K., et al., Intestinal
microbiota development and gestational age in preterm neonates. Sci Rep, 2018.
8(1): p. 2453.
165 Arora, T. and F. Backhed,
The gut microbiota and metabolic disease: current understanding and future perspectives. J Intern Med,
2016. 280(4): p. 339-49.
166 Cox, L.M., et al., Altering the
intestinal microbiota during a critical developmental window has lasting metabolic consequences.
Cell, 2014. 158(4): p. 705-721.
167 Stoll, B.J., et al., Early onset
neonatal sepsis: the burden of group B Streptococcal and E. coli disease continues. Pediatrics, 2011.
127(5): p. 817-26.
168 Gibson, M.K., T.S. Crofts, and G. Dantas, Antibiotics
and the developing infant gut microbiota and resistome.
Curr Opin Microbiol, 2015. 27: p. 51-6.
169 Bokulich, N.A., et al.,
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods,
2013. 10(1): p. 57-9.
170 Nadkarni, M.A., et al.,
Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set.
Microbiology, 2002. 148 (Pt 1): p. 257-66. 171 Delroisse, J.M., et al., Quantification of Bifidobacterium spp. and Lactobacillus spp. in rat fecal samples by real-time PCR. Microbiol Res, 2008.
163(6): p. 663-70.
152 Fricke, W.F., The more the
merrier? Reduced fecal microbiota diversity in preterm infants treated with antibiotics. J Pediatr, 2014.
165(1): p. 8-10.
153 Groer, M.W., et al.,
Development of the preterm infant gut microbiome: a research priority.
Microbiome, 2014. 2: p. 38.
154 Hemels, M.A., et al.,
Prevention of neonatal late- onset sepsis associated with the removal of percutaneously inserted central venous catheters in preterm infants. Pediatr
Crit Care Med, 2011. 12(4): p. 445-8.
155 Reynolds, G.E., S.B. Tierney, and J.M. Klein,
Antibiotics Before Removal of Percutaneously Inserted Central Venous Catheters Reduces Clinical Sepsis in Premature Infants. J
Pediatr Pharmacol Ther, 2015. 20(3): p. 203-9.
156 Martin, R., et al., Early-Life
Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota. PLoS One,
2016. 11(6): p. e0158498.
157 Mshvildadze, M., et al.,
Intestinal microbial ecology in premature infants assessed with non-culture- based techniques. J Pediatr,
2010. 156(1): p. 20-5.
158 Westerbeek, E.A., et al.,
The intestinal bacterial colonisation in preterm infants: a review of the literature. Clin Nutr, 2006.
25(3): p. 361-8.
159 Zwittink, R.D., 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.
160 Ramiro Garcia, J., et al.,
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes. F1000Research,
2016.
161 Turroni, F., et al.,
Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life
Sci, 2018. 75(1): p. 103-118.
142 Edgar, R.C., Search
and clustering orders of magnitude faster than BLAST. Bioinformatics,
2010. 26(19): p. 2460-1.
143 Quast, C., et al., The SILVA
ribosomal RNA gene database project: improved data processing and web- based tools. Nucleic Acids
Res, 2013. 41(Database issue): p. D590-6.
144 Jiang, P., et al., Intestinal
proteome changes during infant necrotizing enterocolitis. Pediatr Res,
2013. 73(3): p. 268-76.
145 Knight, J.M., et al.,
Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing.
Sci Rep, 2014. 4: p. 5453.
146 Jaile, J.C., et al., Benign
gaseous distension of the bowel in premature infants treated with nasal continuous airway pressure: a study of contributing factors. AJR Am J
Roentgenol, 1992. 158(1): p. 125-7.
147 Shaw, A.G., et al., Late-
Onset Bloodstream Infection and Perturbed Maturation of the Gastrointestinal Microbiota in Premature Infants. PLoS
One, 2015. 10(7): p. e0132923.
148 Delgado, S., A.B. Florez, and B. Mayo,
Antibiotic susceptibility of Lactobacillus and Bifidobacterium species from the human gastrointestinal tract. Curr Microbiol, 2005. 50(4): p. 202-7. 149 Moubareck, C., et al., Antimicrobial susceptibility of bifidobacteria. J Antimicrob Chemother, 2005. 55(1): p. 38-44.
150 Mangin, I., et al., Amoxicillin
treatment modifies the composition of Bifidobacterium species in infant intestinal microbiota.
Anaerobe, 2010. 16(4): p. 433-8.
151 Arboleya, S., et al.,
Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics. J Pediatr, 2015. 166(3): p. 538-44. 131 Kolmeder, C.A., et al., Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One,
2012. 7(1): p. e29913.
132 Rappsilber, J., M. Mann, and Y. Ishihama, Protocol
for micro-purification, enrichment, pre- fractionation and storage of peptides for proteomics using StageTips. Nat Protoc,
2007. 2(8): p. 1896-906.
133 Lu, J., et al., Filter-aided
sample preparation with dimethyl labeling to identify and quantify milk fat globule membrane proteins.
J Proteomics, 2011. 75(1): p. 34-43.
134 Vizcaino, J.A., et al.,
2016 update of the PRIDE database and its related tools. Nucleic Acids Res,
2016. 44(22): p. 11033.
135 Cox, J., et al., Andromeda:
a peptide search engine integrated into the MaxQuant environment.
J Proteome Res, 2011. 10(4): p. 1794-805.
136 Schwanhausser, B., et al.,
Global quantification of mammalian gene expression control. Nature, 2011.
473(7347): p. 337-42.
137 Moles, L., et al., Bacterial
diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life. PLoS One,
2013. 8(6): p. e66986.
138 Sim, K., et al., Improved
detection of bifidobacteria with optimised 16S rRNA- gene based pyrosequencing.
PLoS One, 2012. 7(3): p. e32543.
139 Caporaso, J.G., et al.,
QIIME allows analysis of high-throughput community sequencing data. Nat
Methods, 2010. 7(5): p. 335-6.
140 Bragg, L., et al., Fast,
accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods,
2012. 9(5): p. 425-6.
141 Edgar, R.C., et al., UCHIME
improves sensitivity and speed of chimera detection.
Bioinformatics, 2011. 27(16): p. 2194-200.
202 Hoshino, T. and F. Inagaki,
Application of Stochastic Labeling with Random- Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes. PLoS One, 2017.
12(1): p. e0169431.
203 Tourlousse, D.M., et al.,
Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing. Nucleic Acids
Res, 2017. 45(4): p. e23.
204 Human Microbiome Project, C., Structure,
function and diversity of the healthy human microbiome.
Nature, 2012. 486(7402): p. 207-14.
205 Bottacini, F., D. van Sinderen, and M. Ventura,
Omics of bifidobacteria: research and insights into their health-promoting activities. Biochem J, 2017.
474(24): p. 4137-4152.
206 Stewart, C.J., et al.,
Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls.
Microbiome, 2017. 5(1): p. 75.
207 Zhu, D., et al., Effects
of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants. Sci Rep,
2017. 7(1): p. 8025.
208 Hartz, L.E., W. Bradshaw, and D.H. Brandon, Potential
NICU Environmental Influences on the Neonate’s Microbiome: A Systematic Review. Adv Neonatal Care,
2015. 15(5): p. 324-35.
209 Nogacka, A.M., et al., Early
microbiota, antibiotics and health. Cell Mol Life Sci,
2018. 75(1): p. 83-91.
210 WHO, Recommendations
for Prevention and Treatment of Maternal Peripartum Infections. 2015:
Geneva.
211 Aloisio, I., et al.,
Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions. Appl Microbiol
Biotechnol, 2016. 100(12): p. 5537-46.
192 Mueller, S., et al.,
Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross- sectional study. Appl
Environ Microbiol, 2006. 72(2): p. 1027-33.
193 Guilloteau, P., et al.,
Nutritional programming of gastrointestinal tract development. Is the pig a good model for man? Nutr
Res Rev, 2010. 23(1): p. 4-22.
194 Hays, S., et al., Probiotics
and growth in preterm infants: A randomized controlled trial, PREMAPRO study. Clin
Nutr, 2016. 35(4): p. 802-11.
195 Szajewska, H. and A. Chmielewska, Growth
of infants fed formula supplemented with Bifidobacterium lactis Bb12 or Lactobacillus GG: a systematic review of randomized controlled trials. BMC Pediatr, 2013. 13: p. 185.
196 Aceti, A., et al., Probiotics
and Time to Achieve Full Enteral Feeding in Human Milk-Fed and Formula-Fed Preterm Infants: Systematic Review and Meta-Analysis.
Nutrients, 2016. 8(8).
197 Robin, J.D., et al.,
Comparison of DNA Quantification Methods for Next Generation Sequencing. Sci Rep, 2016.
6: p. 24067.
198 Nagpal, R., et al.,
Ontogenesis of the Gut Microbiota Composition in Healthy, Full-Term, Vaginally Born and Breast-Fed Infants over the First 3 Years of Life: A Quantitative Bird’s-Eye View. Front Microbiol, 2017.
8: p. 1388.
199 Vandeputte, D., et al.,
Quantitative microbiome profiling links gut community variation to microbial load. Nature, 2017.
551(7681): p. 507-511.
200 Props, R., et al., Absolute
quantification of microbial taxon abundances. ISME J,
2017. 11(2): p. 584-587.
201 Boers, S.A., J.P. Hays, and R. Jansen, Novel micelle
PCR-based method for accurate, sensitive and quantitative microbiota profiling. Sci Rep, 2017.
7: p. 45536. 181 Hariharan, N., A. Shoemaker, and S. Wagner, Pathophysiology of hypertension in preeclampsia. Microvasc Res, 2017. 109: p. 34-37.
182 Khan, A.M., S.K. Morris, and Z.A. Bhutta, Neonatal
and Perinatal Infections.
Pediatr Clin North Am, 2017. 64(4): p. 785-798.
183 Shane, A.L., P.J. Sanchez, and B.J. Stoll, Neonatal
sepsis. Lancet, 2017.
390(10104): p. 1770-1780.
184 Schulman, J., et al.,
Neonatal intensive care unit antibiotic use. Pediatrics,
2015. 135(5): p. 826-33.
185 Forsgren, M., et al., Late
preterm birth has direct and indirect effects on infant gut microbiota development during the first six months of life. Acta Paediatr, 2017.
106(7): p. 1103-1109.
186 Gregory, K.E., et al.,
Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants. Microbiome, 2016.
4(1): p. 68.
187 Clarke, G., et al., Priming
for health: gut microbiota acquired in early life regulates physiology, brain and behaviour. Acta
Paediatr, 2014. 103(8): p. 812-9.
188 Klindworth, A., et al.,
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res,
2013. 41(1): p. e1.
189 Bizzarro, M.J., et al.,
Neonatal sepsis 2004- 2013: the rise and fall of coagulase-negative staphylococci. J Pediatr,
2015. 166(5): p. 1193-9.
190 Cortese, F., et al., Early and
Late Infections in Newborns: Where Do We Stand? A Review. Pediatr Neonatol,
2016. 57(4): p. 265-73.
191 Markle, J.G., et al., Sex
differences in the gut microbiome drive hormone- dependent regulation of autoimmunity. Science,
2013. 339(6123): p. 1084-8.
172 Matsuda, K., et al.,
Establishment of an analytical system for the human fecal microbiota, based on reverse transcription-quantitative PCR targeting of multicopy rRNA molecules. Appl
Environ Microbiol, 2009. 75(7): p. 1961-9.
173 Patel, C.B., et al., Q-PCR
Based Culture-Independent Enumeration and Detection of Enterobacter: An Emer- ging Environmental Human Pathogen in Riverine Systems and Potable Water. Front
Microbiol, 2016. 7: p. 172.
174 Llewelyn, M.J., et al., The
antibiotic course has had its day. BMJ, 2017. 358: p. j3418.
175 Arias, C.A. and B.E. Murray, The rise of the
Enterococcus: beyond vancomycin resistance.
Nat Rev Microbiol, 2012. 10(4): p. 266-78.
176 Gilmore, M.S., F. Lebreton, and W. van Schaik, Genomic
transition of enterococci from gut commensals to leading causes of multidrug- resistant hospital infection in the antibiotic era. Curr
Opin Microbiol, 2013. 16(1): p. 10-6.
177 Gensollen, T., et al., How
colonization by microbiota in early life shapes the immune system. Science,
2016. 352(6285): p. 539-44.
178 Collado, M.C., et al.,
Effect of mother’s weight on infant’s microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy. Am J Clin
Nutr, 2010. 92(5): p. 1023-30.
179 Fouhy, F., 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): p. 5811-20. 180 Makino, H., et al., Transmission of intestinal Bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism. Appl
212 Jaureguy, F., et al., Effects
of intrapartum penicillin prophylaxis on intestinal bacterial colonization in infants. J Clin Microbiol,
2004. 42(11): p. 5184-8.
213 Lemas, D.J., et al.,
Exploring the contribution of maternal antibiotics and breastfeeding to development of the infant microbiome and pediatric obesity. Semin Fetal
Neonatal Med, 2016. 21(6): p. 406-409.
214 Li, S., et al., Antibiotic
Prevention for Maternal Group B Streptococcal Colonization on Neonatal GBS-Related Adverse Outcomes: A Meta- Analysis. Front Microbiol,
2017. 8: p. 374.
215 Murk, W., K.R. Risnes, and M.B. Bracken, Prenatal
or early-life exposure to antibiotics and risk of childhood asthma: a systematic review.
Pediatrics, 2011. 127(6): p. 1125-38.
216 Raymond, S.L., et al., Impact
of Early-Life Exposures to Infections, Antibiotics, and Vaccines on Perinatal and Long-term Health and Disease. Front Immunol,
2017. 8: p. 729.
217 WHO, Global strategy
for infant and young child feeding. 2003.
218 Neu, J. and J. Rushing,
Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis. Clin Perinatol,
2011. 38(2): p. 321-31.
219 Dominguez-Bello, M.G., et al., Partial restoration of the
microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med, 2016.
22(3): p. 250-3.
220 Fransen, F., et al., The
Impact of Gut Microbiota on Gender-Specific Differences in Immunity. Front Immunol,
2017. 8: p. 754.
221 Ingemarsson, I., Gender
aspects of preterm birth.
BJOG, 2003. 110 Suppl 20: p. 34-8.
222 Zhao, D., et al., Gender
Differences in Infant Mortality and Neonatal Morbidity in Mixed-Gender Twins. Sci Rep, 2017. 7(1):
p. 8736.
223 Liu, J., et al., Remodeling
of the gut microbiota and structural shifts in Preeclampsia patients in South China. Eur J Clin
Microbiol Infect Dis, 2017. 36(4): p. 713-719.
224 Contreras, A., et al.,
Periodontitis is associated with preeclampsia in pregnant women.
J Periodontol, 2006. 77(2): p. 182-8.
225 Huang, X., et al., Maternal
periodontal disease and risk of preeclampsia: a meta- analysis. J Huazhong Univ
Sci Technolog Med Sci, 2014. 34(5): p. 729-35.
226 Nabet, C., et al., Maternal
periodontitis and the causes of preterm birth: the case- control Epipap study.
J Clin Periodontol, 2010. 37(1): p. 37-45.
227 Amarasekara, R., et al.,
Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia. J Obstet
Gynaecol Res, 2015. 41(5): p. 662-9.
228 Barak, S., et al., Evidence
of periopathogenic microorganisms in placentas of women with preeclampsia. J Periodontol, 2007. 78(4): p. 670-6. 229 Mostajeran, F. and B. Arbabi, Is there any
difference between preeclamptic and healthy pregnant women regarding the presence of periopathogenic bacteria in the placenta? Int J Prev
Med, 2013. 4(3): p. 322-6.