Impact of early life diet on microbiome development & later health

Microbial colonization of the new-born is essential for the development of the physiological homeostasis of the host. Perturbations of early-life colonization may have long-lasting effects on host health; specific alterations seem to precede the development of disease, including both communicable and non-communicable diseases. Thus, early microbiota establishment has a profound effect on long-term well-being, therefore representing a critical opportunity for microbiota modulation. Perhaps with the exception of delivery mode and breast/formula-feeding, little was known about the influence of early-life factors on the microbiota establishment. In this context the EarlyMicroHealth project aimed at at unravelling the process of intestinal microbiota establishment in infants and to deduce ways to positively modulate this process. This was done by a longitudinal cohort study, evaluating factors, such as gestational age, antibiotics exposure, etc., that negatively impact early-life microbiota development and the impact of diet and nutrition during the first years of life in driving this process. In a second step the impact of interventions, such as omega three fatty acids or probiotics, in minimizing the impact of these factors was assessed. To achieve this aim we formed a multidisciplinary consortium comprising 5 partners from 4 European countries representing: microbiologists, nutritionists, neonatologists, paediatricians, experts in OMICs and Next-Generation Sequencing and bio-informaticians. The exhaustive analyses of the infant microbiome (including phageome, resistome, etc.) and its combination and integration with clinical and nutritional data allowed determining the impact of different early factors on the microbiota development. The knowledge and tools generated within the project offer opportunities for a stronger European Research Area and increasing European competitiveness on the development and commercialization of microbiota-modulating products for infancy.


Partner OrganizationPartner Country
Wageningen UniversityNetherlands
University College CorkIreland
Complutense University of MadridSpain
Università degli Studi di ParmaItaly



The project has studies the impact of early factors, feeding and postweaning nutrition on the development of the microbiome. By doing this the project has;

  • Developed bioinformatic tools for ITS-based profiling of Bifidobacterium genus species/subspecies and for phageome analyses.
  • Developed food composition tables for commercial foods targeted to infants between 0 and 12 months of age.
  • Identified by first time a phase variation shufflon in bifidobacteria
  • Identified differences on microbiota development between preterm and fullterm neonates
  • Unravelled the effects of intrapartum antimicrobial prophylaxis on the neonatal microbiome
  • Determined the impact of antibiotic exposure during the 1st year of life on microbiome development.
  • Demonstrated the vertical transmission of microorganisms and bacteriophages,
  • Underlined the relationship between early microbiota and weight gain in preterm infants.
  • Determined the interaction nutrition-microbiome development during the first years of life.


Title: Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study
Author: Arboleya, S., Sánchez, B., Solís, G., Fernández, N., Suárez, M., Hernández-Barranco, A.M., Milani, C., Margolles, A., de Los Reyes-Gavilán, C.G., Ventura, M., Gueimonde M.
Link: https://doi.org/10.3390/ijms17050649
Title: Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers.
Author: Duranti, S., Gaiani, F., Mancabelli, L., Milani, C., Grandi, A., Bolchi, A., Santoni, A., Lugli, G., Ferrario, C., Mangifesta, M., Viappiani, A., Bertoni, S., Vivo, V., Serafini, F., Barbaro, M. R., Fugazza, A., Barbara, G., Gioiosa, L., Palanza, P., Cantoni, A. M., de'Angelis, G.L., Barocelli, E., de' Angelis, N., van Sinderen, D., Ventura, M., Turroni, F. 2016.
Link: https://doi.org/10.1093/femsec/fiw191
Title: Perinatal microbiomes’s influence on preterm birth and preterms’s health: influencing factors and modulation strategies.
Author: Ruiz, L., Moles, L., Gueimonde, M., Rodriguez, J.M.
Link: https://doi.org/10.1097/mpg.0000000000001196
Title: Early gut colonization of preterm infants. Effect of enteral feeding tubes
Author: Gómez, M., Moles, L., Melgar, A., Ureta, N., Bustos, G., Fernández, L., Rodríguez, J.M., Jiménez, E.
Link: https://doi.org/10.1097/mpg.0000000000001104
Title: Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age
Author: Lugli, G.A., Milani, C., Mancabelli, L., Turroni, F., Ferrario, C., Duranti, S., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1186/s40168-016-0221-y
Title: Intestinal microbiota and weight-gain in preterm neonates
Author: Arboleya S., Martinez-Camblor P., Solis G., Suárez M., Fernández N., de los Reyes-Gavilán C.G., Gueimonde M.
Link: https://doi.org/10.3389/fmicb.2017.00183
Title: Omics of bifidobacteria: Research and insights into their health promoting activities
Author: Bottacini, F., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1042/bcj20160756
Title: Safety of Novel Microbes for Human Consumption: Practical Examples of Assessment in the European Union
Author: Brodmann T., Endo A., Gueimonde M., Vinderola G., Kneifel W., De Vos W.M., Salminen S., Gómez-Gallego C.
Link: https://doi.org/10.3389/fmicb.2017.01725
Title: Obesity and microbiota: an example of an intricate relationship
Author: Duranti, S., Ferrario, C., van Sinderen, D., Ventura, M., Turroni, F.
Link: https://doi.org/10.1186/s12263-017-0566-2
Title: Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission
Author: Duranti, S., Lugli, G.A., Mancabelli, L., Armanini, F., Turroni, F., James, K., Ferretti, K., Gorfer, V., Ferrario, C., Milani, C., Mangifesta, M., Anzalone, R., Zolfo, M., Viappiani, A., Pasolli, E., Bariletti, I., Canto, R., Clementi, R., Cologna, M., Crifò, T., Cusumano, G., Fedi, S., Gottardi, S., Innamorati, C., Masè, C., Postai, D., Savoi, D., Soffiati, M., Tateo, S., Pedrotti, A., Segata, N., Van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1186/s40168-017-0282-6
Title: Bifidobacteria and the infant gut: an example of co-evolution and natural selection
Author: Turroni, F., Milani, C., Duranti, S., Ferrario, C., Lugli, G.A., Mancabelli, L., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1007/s00018-017-2672-0
Title: In vitro fermentation of different fructo-oligosaccharides by Bifidobacterium strains for the selection of synbiotic combinations
Author: Valdes L., Ruas-Madiedo P., Gueimonde M.
Link: https://doi.org/10.1016/j.ijfoodmicro.2016.11.011
Title: Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic-resistance genes in vaginally delivered full-term neonates
Author: Nogacka, A., Salazar, N., Suárez, M., Milani, C., Arboleya, S., Solís, G., Fernández, N., Alaez, Hernández-Barranco, A., de los Reyes-Gavilán, C., Ventura, M., Gueimonde, M.
Link: https://doi.org/10.1186/s40168-017-0313-3
Title: Bifidobacterium vansinderenii sp. nov. isolated from faeces of emperor tamarin (Saguinus imperator)
Author: Duranti, S., Mangifesta, M., Lugli, G.A., Turroni, F., Anzalone, R., Milani, C., Mancabelli, L., Ossiprandi, M.C., Ventura, M.
Link: https://doi.org/10.1099/ijsem.0.002243
Title: How to feed the mammalian gut microbiota: bacterial and metabolic modulation by dietary fibers
Author: Ferrario, C., Statello, R., Carnevali, L., Mancabelli, L., Milani, C., Mangifesta, M., Duranti, S., Lugli, G.A., Jimenez, B., Lodge, S., Viappiani, A., Alessandri, G., Dall'Asta, M., Del Rio, D., Sgoifo, A., Van Sinderen, D., Ventura, M., Turroni, F.
Link: https://doi.org/10.3389/fmicb.2017.01749
Title: Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family
Author: Lugli, G.L., Milani, C., Turroni, F., Duranti, S., Mancabelli, L., Mangifesta, M., Ferrario, C., Modesto, M., Mattarelli, P., Jiří, J., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1186/s12864-017-3955-4
Title: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations. Environ
Author: Mancabelli, L., Milani, C., Lugli, G.A., Turroni, F., Ferrario, C., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1111/1462-2920.13692
Title: Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses
Author: Mancabelli, L., Milani, C., Lugli, G.A., Turroni, F., Mangifesta, M., Viappiani, A., Ticinesi, A., Nouvenne, A., Meschi, T., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1038/s41598-017-10663-w
Title: The first microbial colonizers of the human gut: composition, activities and health implications of the infant gut microbiota
Author: Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado, S., Arboleya, S., Mancabelli, L., Lugli, G.A., Rodriguez, J.M., Bode, L., de Vos, W., Gueimonde, M., Margolles, A., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1128/mmbr.00036-17
Title: Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life
Author: Milani, C., Mangifesta, M., Mancabelli, L., Lugli, G.A., James, K., Duranti, S., Turroni, F., Ferrario, C., Ossiprandi, M.C., van Sinderen, D., Ventura, M
Link: https://doi.org/10.1038/ismej.2017.138
Title: The sortase-dependent fimbriome of the genus Bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue.
Author: Milani, C., Mangifesta, M., Mancabelli, L., Lugli, G.A., Mancino, W., Viappiani, A., Faccini, A., van Sinderen, D., Ventura, M., Turroni, F.
Link: https://doi.org/10.1128/aem.01295-17
Title: Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full term infants
Author: Ravi A., Valdes-Varela L., Borges P.J.A., Gueimonde M., Rudi, K.
Link: https://doi.org/10.1093/femsec/fix158
Title: Tracing mother-infant transmission of bacteriophages by means of a novel tool for analysis of shotgun metagenomics datasets: METAnnotatorX
Author: Milani, C., Casey, E., Lugli, G.A., Moore, R., Kaczorowska, J., Feehily, C., Mangifesta, M., Mancabelli, L., Duranti, S., Turroni, F., Mahony, J., Cotter, P.J., McAuliffe F., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1186/s40168-018-0527-z
Title: Microbiota and derived parameters in fecal samples of infants with non-IgE cow's milk protein allergy under a restricted diet
Author: Díaz M, Guadamuro L, Espinosa-Martos I, Mancabelli L, Jiménez S, Molinos-Norniella C, Pérez-Solis D, Milani C, Rodríguez JM, Ventura M, Bousoño C, Gueimonde M, Margolles A, Díaz JJ, Delgado S
Link: https://doi.org/10.3390/nu10101481
Title: Modulatory effect of three probiotic strains on infants' gut microbial composition and immunological parameters on a placebo-controlled, double-blind, randomised study
Author: De Andrés J, Manzano S, García C, Rodríguez JM, Espinosa-Martos I, Jiménez E.
Link: https://doi.org/10.3920/bm2017.0132
Title: Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gut
Author: Lugli, G.A., Mancino, W., Milani, C., Duranti, S., Turroni, F., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1128/aem.00796-18
Title: The autochthonous microbiota and probiotics: efficacious complements in the fight against infections and the rising of antibiotic resistance
Author: Rodríguez JM, Guarner F, Álvarez-Calatayud G, Suárez E.
Title: Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches
Author: Lugli, G.A., Milani, C., Duranti, S., Alessandri, G., Turroni, F., Mancabelli, L., Tatoni, D., Ossiprandi, M.C., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1186/s13059-019-1711-6
Title: Increased incidence of necrotizing enterocolitis associated with routine administration of InfloranTM in extremely preterm infants
Author: Escribano E , Zozaya C, Madero R; Sánchez L, van Goudoever J , Rodríguez JM, Sáenz de Pipaon M.
Link: https://doi.org/10.3920/bm2017.0098
Title: Early microbiota, antibiotics and health
Author: Nogacka A., Salazar N., Arboleya S., Suárez M., Fernández N., Solís G., de los Reyes-Gavilán C.G., Gueimonde M.
Link: https://doi.org/10.1007/s00018-017-2670-2
Title: In Vitro Characteristics of Phages to Guide 'Real Life' Phage Therapy Suitability
Author: Casey E, van Sinderen D, Mahony J.
Link: https://doi.org/10.3390/v10040163
Title: C-section and the neonatal gut microbiome acquisition: consequences for future health
Author: Arboleya S, Suárez M, Fernández N, Mantecón L, Solís G, Gueimonde M, de Los Reyes-Gavilán CG
Link: https://doi.org/10.1159/000490843
Title: An exploratory search for potential molecular targets responsive to the probiotic Lactobacillus salivarius PS2 in women with mastitis: gene expression profiling vs. interindividual variability
Author: de Andrés J, Jiménez E, Espinosa-Martos I, Rodríguez JM, García-Conesa MT
Link: https://doi.org/10.3389/fmicb.2018.02166
Title: Impact of gut associated bifidobacteria and their phages on health: two sides ofthe same coin?
Author: Mahony J, Lugli GA, van Sinderen D, Ventura M.
Link: https://doi.org/10.1007/s00253-018-8795-x
Title: Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How?
Author: Geerlings SY, Kostopoulos I, de Vos WM, Belzer C.
Link: https://doi.org/10.3390/microorganisms6030075
Title: Characterization and induction of prophages in human gut-associated Bifidobacterium hosts
Author: Mavrich TN, Casey E, Oliveira J, Bottacini F,James K, Franz CMAP, Lugli GA, Neve H, Ventura M, Hatfull GF, Mahony J, van Sinderen D.
Link: https://doi.org/10.1038/s41598-018-31181-3
Title: Dissecting the evolutionary development of the Bifidobacterium animalis species through comparative genomics analyses
Author: Lugli, G.A., Mancino, W., Milani, C., Duranti, S., Mancabelli, L., Napoli, S., Mangifesta, M., Viappiani, A., Anzalone, R., Longhi, G., van Sinderen, D., Ventura, M., Turroni, F.
Link: https://doi.org/10.1128/aem.02806-18
Title: Nutritional composition of processed baby food targeted at infants from 0-12 months
Author: Gómez-Martín, M., Arboleya, S., Gueimonde, M., Gonzalez, S.
Link: http://dx.doi.org/10.1016/j.jfca.2019.03.009
Title: Unveiling genomic diversity among members of the Bifidobacterium pseudolongum species, a widely distributed gut commensal of the animal kingdom
Author: Lugli, G.A., Duranti, S., Albert, K., Mancabelli, L., Napoli, S., Viappiani, A., Anzalone, R., Longhi, G., Milani, C., Turroni, F., Alessandri, G., Sela, D., van Sinderen, D., and Ventura, M.
Link: https://doi.org/10.1128/aem.03065-18
Title: Compositional assessment of bacterial communities in probiotic supplements by means of metagenomic techniques
Author: Lugli, G.A., Mangifesta, M., Mancabelli, L., Milani, C., Turroni, F., Viappiani, A., van Sinderen, D., Ventura, M.
Link: https://doi.org/10.1016/j.ijfoodmicro.2019.01.011
Title: Health benefits conferred by the human gut microbiota during infancy
Author: Ventura, M., Milani, C., Lugli, G.A., van Sinderen D.
Link: https://doi.org/10.1111/1751-7915.13334



Project number:
Duration: 100%
Duration: 100 %
Related funding round:
Project lead and secretary:
Miguel Gueimonde