Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants

R: A Language and Environment for Statistical Computing

R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,893

DADA2: High–resolution sample inference from Illumina amplicon data

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055

lavaan : An R Package for Structural Equation Modeling

Rosseel, Y. (2012) · Journal of Statistical Software · doi:10.18637/jss.v048.i02 · Cited by 27,955

vegan: Community Ecology Package

Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,942

Classification and Regression by randomForest

Liaw, A. I., & Wiener, M. C. (2007) · Cited by 18,594

Simultaneous Inference in General Parametric Models

Hothorn, T., Bretz, F., & Westfall, P. H. (2008) · Biometrical Journal · doi:10.1002/bimj.200810425 · Cited by 14,265

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

Gu, Z., Eils, R., & Schlesner, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw313 · Cited by 10,037

Fitting Linear Mixed-Effects Models Using lme4Preprint

Bates, D. M., Maechler, M., Bolker, B. M., & Walker, S. (2014) · arXiv (Cornell University) · doi:10.3929/ethz-b-000105397 · Cited by 9,435

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01043-13 · Cited by 7,246

Estimating the Number of Clusters in a Data Set Via the Gap Statistic

Tibshirani, R., Walther, G., & Hastie, T. (2001) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/1467-9868.00293 · Cited by 6,205

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579

Mechanisms of Succession in Natural Communities and Their Role in Community Stability and Organization

Connell, J. H., & Slatyer, R. O. (1977) · The American Naturalist · doi:10.1086/283241 · Cited by 4,351

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Pang, Z., Chong, J., Zhou, G., Morais, D. A. D. L., Chang, L., Barrette, M., Gauthier, C., Jacques, P., Li, S., & Xia, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab382 · Cited by 3,972

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Nilsson, R. H., Larsson, K.-H., Taylor, A. F. S., Bengtsson‐Palme, J., Jeppesen, T. S., Schigel, D., Kennedy, P. G., Picard, K. T., Glöckner, F. O., Tedersoo, L., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1022 · Cited by 3,660

A taxonomic note on the genus lactobacillus: description of 23 novel genera, emended description of the genus lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313

Succession of microbial consortia in the developing infant gut microbiome

Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540

Bifidobacteria can protect from enteropathogenic infection through production of acetate

Fukuda, S., Toh, H., Hase, K., Oshima, K., Nakanishi, Y., Yoshimura, K., Tobe, T., Clarke, J. M., Topping, D. L., Suzuki, T., et al. (2011) · Nature · doi:10.1038/nature09646 · Cited by 2,387

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

Ihrmark, K., Bödeker, I. T. M., Cruz-Martínez, K., Friberg, H., Kubartová, A., Schenck, J., Strid, Y., Stenlid, J., Durling, M. B., Clemmensen, K. E., et al. (2012) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2012.01437.x · Cited by 2,096

Saturated Fatty Acids, but Not Unsaturated Fatty Acids, Induce the Expression of Cyclooxygenase-2 Mediated through Toll-like Receptor 4

Lee, J. Y., Sohn, K. H., Rhee, S. H., & Hwang, D. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m011695200 · Cited by 1,299

Bifidobacteria and Their Role as Members of the Human Gut Microbiota

O’Callaghan, A. A., & van Sinderen, D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00925 · Cited by 1,160

Consequences of bile salt biotransformations by intestinal bacteria

Ridlon, J. M., Harris, S. C., Bhowmik, S., Kang, D.-J., & Hylemon, P. B. (2016) · Gut Microbes · doi:10.1080/19490976.2015.1127483 · Cited by 1,128

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

Palarea‐Albaladejo, J., & Fernández, J. A. M. (2015) · Chemometrics and Intelligent Laboratory Systems · doi:10.1016/j.chemolab.2015.02.019 · Cited by 963

Interleukin-22: Immunobiology and Pathology

Dudakov, J. A., Hanash, A. M., & van den Brink, M. R. M. (2015) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032414-112123 · Cited by 939

Two Routes of Metabolic Cross-Feeding between Bifidobacterium adolescentis and Butyrate-Producing Anaerobes from the Human Gut

Belenguer, A., Duncan, S. H., Calder, A. G., Holtrop, G., Louis, P., Lobley, G. E., & Flint, H. J. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3593-3599.2006 · Cited by 856

Bifidobacteria-mediated immune system imprinting early in life

Henrick, B. M., Rodriguez, L., Lakshmikanth, T., Pou, C., Henckel, E., Arzoomand, A., Olin, A., Wang, J., Mikeš, J., Tan, Z., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.030 · Cited by 836

The R Package geepack for Generalized Estimating Equations

Højsgaard, S., Halekoh, U., & Yan, J. (2005) · RePEc: Research Papers in Economics · Cited by 805

The human gut microbiome: ecology and recent evolutionary changes

Walter, J., & Ley, R. (2011) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090110-102830 · Cited by 720

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis

Pammi, M., Cope, J., Tarr, P. I., Warner, B. B., Morrow, A. L., Mai, V., Gregory, K. E., Kroll, J. S., McMurtry, V., Ferris, M. J., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0248-8 · Cited by 708

Stereotypic Immune System Development in Newborn Children

Olin, A., Henckel, E., Chen, Y., Lakshmikanth, T., Pou, C., Mikeš, J., Gustafsson, A., Bernhardsson, A. K., Zhang, C., Bohlin, K., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.045 · Cited by 708

Metabolomic Analysis and Visualization Engine for LC−MS Data

Melamud, E., Vastag, L., & Rabinowitz, J. D. (2010) · Analytical Chemistry · doi:10.1021/ac1021166 · Cited by 615

The ecology of restoration: historical links, emerging issues and unexplored realms

Young, T. P., Petersen, D., & Clary, J. J. (2005) · Ecology Letters · doi:10.1111/j.1461-0248.2005.00764.x · Cited by 612

Patterned progression of bacterial populations in the premature infant gut

Rosa, P. S. L., Warner, B. B., Zhou, Y., Weinstock, G. M., Sodergren, E. J., Hall-Moore, C. M., Stevens, H. J., Bennett, W. E., Shaikh, N., Linneman, L. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1409497111 · Cited by 586

LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine

Clasquin, M. F., Melamud, E., & Rabinowitz, J. D. (2012) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1411s37 · Cited by 513

Establishment and development of intestinal microbiota in preterm neonates

Arboleya, S., Binetti, A. G., Salazar, N., Fernández, N., Sánchez, G. S., Hernández‐Barranco, A. M., Margollés, A., Reyes‐Gavilán, C. G. D. L., & Gueimonde, M. (2011) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2011.01261.x · Cited by 468

Role of priority effects in the early-life assembly of the gut microbiota

Sprockett, D., Fukami, T., & Relman, D. A. (2018) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.173 · Cited by 419

Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data

Gloor, G. B., & Reid, G. (2016) · Canadian Journal of Microbiology · doi:10.1139/cjm-2015-0821 · Cited by 380

Multi-kingdom ecological drivers of microbiota assembly in preterm infants

Rao, C., Coyte, K. Z., Bainter, W., Geha, R. S., Martin, C. R., & Rakoff-Nahoum, S. (2021) · Nature · doi:10.1038/s41586-021-03241-8 · Cited by 364

Cross-Feeding between Bifidobacterium longum BB536 and Acetate-Converting, Butyrate-Producing Colon Bacteria during Growth on Oligofructose

Falony, G., Vlachou, A., Verbrugghe, K., & Vuyst, L. D. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.01296-06 · Cited by 362

Intestinal microbiota development and gestational age in preterm neonates

Korpela, K., Blakstad, E. W., Moltu, S. J., Strømmen, K., Nakstad, B., Rønnestad, A. E., Brække, K., Iversen, P. O., Drevon, C. A., & de Vos, W. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-20827-x · Cited by 313

Oral Supplementation with Lactobacillus casei Subspecies rhamnosus Prevents Enteric Colonization by Candida Species in Preterm Neonates: A Randomized Study

Manzoni, P., Mostert, M., Leonessa, M., Priolo, C., Farina, D., Monetti, C., Latino, M. A., & Gomirato, G. (2006) · Clinical Infectious Diseases · doi:10.1086/504324 · Cited by 305

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting

Arrieta, M., Arévalo‐Cortes, A., Stiemsma, L. T., Dimitriu, P. A., Chico, M. E., Loor, S., Vaca, M. G., Boutin, R. C. T., Morien, E., Jin, M., et al. (2017) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.08.041 · Cited by 272

Delivery Mode Affects Stability of Early Infant Gut Microbiota

Mitchell, C. M., Mazzoni, C., Hogstrom, L. J., Bryant, A., Bergerat, A., Cher, A., Pochan, S., Herman, P., Carrigan, M., Sharp, K., et al. (2020) · Cell Reports Medicine · doi:10.1016/j.xcrm.2020.100156 · Cited by 252

Problems with the concept of gut microbiota dysbiosis

Brüssow, H. (2020) · Microbial Biotechnology · doi:10.1111/1751-7915.13479 · Cited by 250

Toll-like receptor 4–mediated lymphocyte influx induces neonatal necrotizing enterocolitis

Egan, C. E., Sodhi, C. P., Good, M. L., Lin, J., Jia, H., Yamaguchi, Y., Lu, P., Ma, C., Branca, M. F., Weyandt, S., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci83356 · Cited by 238

Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study

Alcon-Giner, C., Dalby, M. J., Caim, S., Ketskemety, J., Shaw, A., Sim, K., Lawson, M. A., Kiu, R., Leclaire, C., Chalklen, L., et al. (2020) · Cell Reports Medicine · doi:10.1016/j.xcrm.2020.100077 · Cited by 235

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

Frese, S. A., Hutton, A. A., Contreras, L. N., Shaw, C. A., Palumbo, M. C., Casaburi, G., Xu, G., Davis, J. C. C., Lebrilla, C. B., Henrick, B. M., et al. (2017) · mSphere · doi:10.1128/msphere.00501-17 · Cited by 231

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

Stewart, C. J., Embleton, N. D., Marrs, E. C. L., Smith, D. P., Nelson, A., Abdulkadir, B., Skeath, T., Petrosino, J. F., Perry, J. D., Berrington, J. E., et al. (2016) · Microbiome · doi:10.1186/s40168-016-0216-8 · Cited by 222

To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes

Walter, J., Maldonado-Gómez, M. X., & Martínez, I. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.08.008 · Cited by 203

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly

Martínez, I., Maldonado-Gomez, M. X., Gomes-Neto, J. C., Kittana, H., Ding, H., Schmaltz, R., Joglekar, P., Cardona, R. J., Marsteller, N. L., Kembel, S. W., et al. (2018) · eLife · doi:10.7554/elife.36521 · Cited by 199

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

Laforest‐Lapointe, I., & Arrieta, M. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00788 · Cited by 195

Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium

Egan, M., Motherway, M. O., Kilcoyne, M., Kane, M., Joshi, L., Ventura, M., & van Sinderen, D. (2014) · BMC Microbiology · doi:10.1186/s12866-014-0282-7 · Cited by 193

Infant and Adult Gut Microbiome and Metabolome in Rural Bassa and Urban Settlers from Nigeria

Ayeni, F. A., Biagi, E., Rampelli, S., Fiori, J., Soverini, M., Audu, H. J., Cristino, S., Caporali, L., Schnorr, S. L., Carelli, V., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.018 · Cited by 193

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota

Davis, J. C. C., Lewis, Z. T., Krishnan, S., Bernstein, R. M., Moore, S. E., Prentice, A. M., Mills, D. A., Lebrilla, C. B., & Zivkovic, A. M. (2017) · Scientific Reports · doi:10.1038/srep40466 · Cited by 187

Generalized estimating equations: A pragmatic and flexible approach to the marginal GLM modelling of correlated data in the behavioural sciences

Pekár, S., & Brabec, M. (2018) · Ethology · doi:10.1111/eth.12713 · Cited by 178

Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants

Costello, E. K., Carlisle, E. M., Bik, E. M., Morowitz, M. J., & Relman, D. A. (2013) · mBio · doi:10.1128/mbio.00782-13 · Cited by 175

The Preterm Gut Microbiota: An Inconspicuous Challenge in Nutritional Neonatal Care

Henderickx, J. G. E., Zwittink, R. D., van Lingen, R. A., Knol, J., & Belzer, C. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00085 · Cited by 173

Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum

Gotoh, A., Katoh, T., Sakanaka, M., Ling, Y., Yamada, C., Asakuma, S., Urashima, T., Tomabechi, Y., Katayama-Ikegami, A., Kurihara, S., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-32080-3 · Cited by 171

The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth

Chernikova, D. A., Madan, J. C., Housman, M. L., Zain-Ul-Abideen, M., Lundgren, S., Morrison, H. G., Sogin, M. L., Williams, S. M., Moore, J. H., Karagas, M. R., et al. (2018) · Pediatric Research · doi:10.1038/s41390-018-0022-z · Cited by 168

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis

Wandro, S., Osborne, S., Enriquez, C., Bixby, C., Arrieta, A. C., & Whiteson, K. (2018) · mSphere · doi:10.1128/msphere.00104-18 · Cited by 162

Cytokines associated with necrotizing enterocolitis in extremely-low-birth-weight infants

Maheshwari, A., Schelonka, R. L., Dimmitt, R. A., Carlo, W. A., Muñoz, B., Das, A., McDonald, S. A., Thorsen, P., Skogstrand, K., HOUGAARD, D. M., et al. (2014) · Pediatric Research · doi:10.1038/pr.2014.48 · Cited by 157

Discrete Time Markov Chains with R

Spedicato, G. (2017) · The R Journal · doi:10.32614/rj-2017-036 · Cited by 148

Plasma 3-Nitrotyrosine Is Elevated in Premature Infants Who Develop Bronchopulmonary Dysplasia

Banks, B. A., Ischiropoulos, H., McClelland, M., Ballard, P. L., & Ballard, R. A. (1998) · PEDIATRICS · doi:10.1542/peds.101.5.870 · Cited by 142

Breast Milk Lipids and Fatty Acids in Regulating Neonatal Intestinal Development and Protecting against Intestinal Injury

Ramiro‐Cortijo, D., Singh, P., Liu, Y., Medina‐Morales, E., Yakah, W., Freedman, S. D., & Martin, C. R. (2020) · Nutrients · doi:10.3390/nu12020534 · Cited by 141

The immunological landscape in necrotising enterocolitis

Cho, S., Berger, P. J., Nold‐Petry, C. A., & Nold, M. F. (2016) · Expert Reviews in Molecular Medicine · doi:10.1017/erm.2016.13 · Cited by 113

Probiotics Prevent Late-Onset Sepsis in Human Milk-Fed, Very Low Birth Weight Preterm Infants: Systematic Review and Meta-Analysis

Aceti, A., Maggio, L., Beghetti, I., Gori, D., Barone, G., Callegari, M. L., Fantini, M. P., Indrio, F., Meneghin, F., Morelli, L., et al. (2017) · Nutrients · doi:10.3390/nu9080904 · Cited by 106

Use of probiotics and prebiotics in infant feeding

Bertelsen, R. J., Jensen, E. T., & Ringel‐Kulka, T. (2016) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2016.01.001 · Cited by 93

Probiotics for Preterm Neonates: What Will It Take to Change Clinical Practice?

Shlomai, N. O., Deshpande, G. C., Rao, S. C., & Patole, S. (2013) · Neonatology · doi:10.1159/000354891 · Cited by 82

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network

de Goffau, M. C., Jallow, A. T., Sanyang, C., Prentice, A. M., Meagher, N., Price, D. J., Revill, P. A., Parkhill, J., Pereira, D. I. A., & Wagner, J. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01023-6 · Cited by 82

Prevention of Necrotizing Enterocolitis Through Manipulation of the Intestinal Microbiota of the Premature Infant

Vongbhavit, K., & Underwood, M. A. (2016) · Clinical Therapeutics · doi:10.1016/j.clinthera.2016.01.006 · Cited by 79

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies

Shields‐Cutler, R. R., Al-Ghalith, G. A., Yassour, M., & Knights, D. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00785 · Cited by 79

Fecal Metabolomics of Healthy Breast-Fed versus Formula-Fed Infants before and during In Vitro Batch Culture Fermentation

Chow, J., Panasevich, M. R., Alexander, D. C., Boler, B. M. V., Serao, M. C. R., Faber, T. A., Bauer, L. L., & Fahey, G. C., Jr. (2014) · Journal of Proteome Research · doi:10.1021/pr500011w · Cited by 74

The role of the preterm intestinal microbiome in sepsis and necrotising enterocolitis

Masi, A. C., & Stewart, C. J. (2019) · Early Human Development · doi:10.1016/j.earlhumdev.2019.104854 · Cited by 72

Detection of Pro- and Anti-Inflammatory Cytokines in Stools of Patients with Inflammatory Bowel Disease

Saiki, T. (1998) · Scandinavian Journal of Gastroenterology · doi:10.1080/00365529850171891 · Cited by 71

Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial

for the ProPrems Study Group, Plummer, E. L., Bulach, D., Murray, G. L., Jacobs, S. E., Tabrizi, S. N., & Garland, S. M. (2018) · BMC Microbiology · doi:10.1186/s12866-018-1326-1 · Cited by 70

Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts

Cheng, C. C., Duar, R. M., Lin, X. B., Pérez-Muñoz, M. E., Tollenaar, S. L., Oh, J., van Pijkeren, J., Li, F., van Sinderen, D., Gänzle, M. G., et al. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.00190-20 · Cited by 67

Exploring Amino Acid Auxotrophy in Bifidobacterium bifidum PRL2010

Ferrario, C., Duranti, S., Milani, C., Mancabelli, L., Lugli, G. A., Turroni, F., Mangifesta, M., Viappiani, A., Ossiprandi, M. C., van Sinderen, D., et al. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01331 · Cited by 64

Distinct Gut Microbiota and Metabolite Profiles Induced by Different Feeding Methods in Healthy Chinese Infants

Li, N., Yan, F., Wang, N., Song, Y., Yue, Y., Guan, J., Li, B., & Huo, G. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00714 · Cited by 64

Microbiota stability and gastrointestinal tolerance in response to a high-protein diet with and without a prebiotic, probiotic, and synbiotic: A randomized, double-blind, placebo-controlled trial in older women

Ford, A. L., Nagulesapillai, V., Piano, A., Auger, J., Girard, S.-A., Christman, M., Tompkins, T. A., & Dahl, W. J. (2020) · Journal of the Academy of Nutrition and Dietetics · doi:10.1016/j.jand.2019.12.009 · Cited by 63

Interleukin-22 signaling attenuates necrotizing enterocolitis by promoting epithelial cell regeneration

Mihi, B., Gong, Q., Nolan, L. S., Gale, S. E., Goree, M., Hu, E. Z., Lanik, W. E., Rimer, J. M., Liu, V. S., Parks, O. B., et al. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100320 · Cited by 61

Bile Acid Concentrations in Serum and Duodenal Aspirates of Healthy Preterm Infants: Effects of Gestational and Postnatal Age

Boehm, G., Braun, W., Moro, G., & MINOLI, I. (2009) · Biology of the Neonate · doi:10.1159/000244419 · Cited by 59

Oxidative DNA damage induced by nitrotyrosine, a biomarker of inflammation

Murata, M., & Kawanishi, S. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.02.022 · Cited by 55

Probiotics Prevent Candida Colonization and Invasive Fungal Sepsis in Preterm Neonates: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

Hu, H.-J., Zhang, G., Zhang, Q., Shakya, S., & Li, Z. (2016) · Pediatrics & Neonatology · doi:10.1016/j.pedneo.2016.06.001 · Cited by 52

Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b Metabolic Interaction Based on 2′- O -Fucosyl-Lactose Studied in Steady-State Cultures in a Freter-Style Chemostat

Centanni, M., Ferguson, S. A., Sims, I. M., Biswas, A., & Tannock, G. W. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02783-18 · Cited by 49

Pulmonary Nitric Oxide Synthases and Nitrotyrosine: Findings During Lung Development and in Chronic Lung Disease of Prematurity

Sheffield, M. A., Mabry, S. M., Thibeault, D. W., & Truog, W. E. (2006) · PEDIATRICS · doi:10.1542/peds.2006-0195 · Cited by 28

Building Robust Assemblages of Bacteria in the Human Gut in Early Life

Tannock, G. W. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.01449-21 · Cited by 24

Probiotics and Necrotising Enterocolitis: The Devil (as Always) Is in the Detail

Modi, N. (2013) · Neonatology · doi:10.1159/000354909 · Cited by 20

Exposure to Parasitic Protists and Helminths Changes the Intestinal Community Structure of Bacterial Communities in a Cohort of Mother-Child Binomials from a Semirural Setting in Mexico

Partida‐Rodríguez, O., Nieves, M., Laforest‐Lapointe, I., Brown, E., Parfrey, L. W., Reynolds, L., Valadez-Salazar, A., Thorson, L., Moran, P., González, E., et al. (2021) · mSphere · doi:10.1128/msphere.00083-21 · Cited by 16

Emerging issues in probiotic safety: 2023 perspectives

Merenstein, D., Pot, B., Leyer, G., Ouwehand, A. C., Preidis, G. A., Elkins, C. A., Hill, C., Lewis, Z. T., Shane, A. L., Zmora, N., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2185034 · Cited by 481

Toward a Deeper Understanding of Gut Microbiome in Depression: The Promise of Clinical Applicability

Liu, L., Wang, H., Zhang, H., Chen, X., Zhang, Y., Wu, J. Y., Zhao, L., Wang, D., Pu, J., Ji, P., et al. (2022) · Advanced Science · doi:10.1002/advs.202203707 · Cited by 162

A comprehensive review on infant formula: nutritional and functional constituents, recent trends in processing and its impact on infants’ gut microbiota

Bakshi, S., Paswan, V. K., Yadav, S. P., Bhinchhar, B. K., Kharkwal, S., Rose, H., Kanetkar, P., Kumar, V., Al-Zamani, Z. A. S., & Bunkar, D. S. (2023) · Frontiers in Nutrition · doi:10.3389/fnut.2023.1194679 · Cited by 148

Comparing early life nutritional sources and human milk feeding practices: personalized and dynamic nutrition supports infant gut microbiome development and immune system maturation

Ames, S. R., Lotoski, L. C., & Azad, M. B. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2190305 · Cited by 156

Role of Bifidobacterium in Modulating the Intestinal Epithelial Tight Junction Barrier: Current Knowledge and Perspectives

Abdulqadir, R. F., Engers, J., & Al–Sadi, R. (2023) · Current Developments in Nutrition · doi:10.1016/j.cdnut.2023.102026 · Cited by 136

Probiotics to improve the gut microbiome in premature infants: are we there yet?

Mercer, E. M., & Arrieta, M. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2201160 · Cited by 80

Preterm infants fed B. infantis EVC001 Demonstrate Significant Reduction in Intestinal Inflammation via Modulation of Gut Microbiome Composition

Nguyen, M., Holdbrooks, H., Abrantes, M. A., Mishra, P. K., McGuckin, C., Hein, C. T., Chew, S., Brown, H. K., Casaburi, G., Kazi, S., et al. (2021) · PEDIATRICS · doi:10.1542/peds.147.3ma7.722

Effect of probiotic supplementation on the gut microbiota in very preterm infants: a systematic review

Vievermanns, K., Dierikx, T. H., Oldenburger, N. J., van Etten‐Jamaludin, F. S., Niemarkt, H. J., & de Meij, T. G. J. (2024) · Archives of Disease in Childhood Fetal & Neonatal · doi:10.1136/archdischild-2023-326691 · Cited by 11

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants

Beck, L. C., Masi, A. C., Young, G. R., Vatanen, T., Lamb, C. A., Smith, R., Coxhead, J., Butler, A., Marsland, B. J., Embleton, N. D., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01213-w · Cited by 164

Effects of Probiotics on Preterm Infant Gut Microbiota Across Populations: A Systematic Review and Meta-Analysis

He, P., Yu, L., Tian, F., Chen, W., Zhang, H., & Zhai, Q. (2024) · Advances in Nutrition · doi:10.1016/j.advnut.2024.100233 · Cited by 22