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The first years of life represent a window of opportunity to establish proper dietary patterns and to maintain them over time. Our aim was to describe the diet of a cohort of Spanish children, from 2 to 36 months, and to identify the components that could influence the quality of the diet at 24 and 36 months of age. This was a longitudinal prospective study analyzing information from administered questionnaires about general characteristics and food frequency consumption in 97 full-term babies. At 2–3 months of age, only 53.6% of infants were observed to be breastfed. The intake of animal foodstuffs from 12 to 36 months was higher than national recommendations, and the contrary was true for fruits and vegetables. The intake of vitamin D was below European Food Safety Authority recommendations. Moreover, energy intake at 6 months was inversely associated with Mediterranean Diet Score (MDS) at 24 months, whereas vegetables intake was positively associated with MDS at 36 months. These results could be useful in the creation of future guidelines focused on the promotion of breastfeeding and healthy early-life food habits, This work was financed by PCIN-2015-233 (Project EarlyMicroHealth from the EU Joint Program Initiative HDHL) (MINECO/FEDER, UE) and by the University of Oviedo (Diet, Rhythms and Early Acquisition Microbiota (DREAMS) Project; Reference no. 2017/00001/003/005/013). S.A. was the recipient of a postdoctoral Juan de la Cierva Contract (Reference no. IJCI-2017-32156) funded by MCIU/AEI/10.13039/501100011033. M.G-M. was the recipient of a pre-doctoral FPU contract FPU18/03393) funded by the Spanish Ministry of Science, Innovation, and Universities.

Food addiction is characterized by a loss of behavioral control over food intake and is associated with obesity and other eating disorders. The mechanisms underlying this behavioral disorder are largely unknown. We aimed to investigate the changes in miRNA expression promoted by food addiction in animals and humans and their involvement in the mechanisms underlying the behavioral hallmarks of this disorder. We found sharp similitudes between miRNA signatures in the medial prefrontal cortex (mPFC) of our animal cohort and circulating miRNA levels in our human cohort, which allowed us to identify several miRNAs of potential interest in the development of this disorder. Tough decoy (TuD) inhibition of miRNA-29c-3p in the mouse mPFC promoted persistence of the response and enhanced vulnerability to developing food addiction, whereas miRNA-665-3p inhibition promoted compulsion-like behavior and also enhanced food addiction vulnerability. In contrast, we found that miRNA-137-3p inhibition in the mPFC did not lead to the development of food addiction. Therefore, miRNA-29c-3p and miRNA-665-3p could be acting as protective factors with regard to food addiction. We believe the elucidation of these epigenetic mechanisms will lead to advances toward identifying innovative biomarkers and possible future interventions for food addiction and related disorders based on the strategies now available to modify miRNA activity and expression. This work was supported by the Spanish “Ministerio de Ciencia e Innovación (MICIN), Agencia Estatal de Investigación (AEI)” (PID2020-120029GB-I00/MICIN/AEI/10.13039/501100011033, RD21/0009/0019, to RM; SAF2015-68341-R, RTI2018-100968-B-100, and PID2021-1277760B-100, to BC; and SAF2017-84060-R-AEI/FEDER-UE, to LD); the “Generalitat de Catalunya, AGAUR” (2017 SGR-669, to RM; 2017 SGR-734, to JMFR; 2017-SGR-738, to BC); the “ICREA-Acadèmia” (2020, to RM, 2021, to BC, and 2022, to JMFR); the “European Commission-DG Research” (PainFact, H2020-SC1-2019-2-RTD-848099, QSPain Relief, H2020-SC1-2019-2-RTD-848068, to RM; CoCA, H2020-667302, and Eat2beNICE, H2020-728018, to BC); the Spanish “Instituto de Salud Carlos III, RETICS-RTA” (RD16/0017/0020, to RM; FIS PI15/01934, PI18/01022, PI21/01361, to JMFR); the Spanish “Ministerio de Sanidad, Servicios Sociales e Igualdad, Plan Nacional Sobre Drogas” (PNSD- 2021I076, to RM; PNSD-2019I006, to EMG; PNSD-2017I050, to BC; PNSD-2020I042, to NFC); the “Fundació La Marató-TV3” (2016/20-30, to EMG); the European Regional Development Fund (project no. 01.2.2-LMT-K-718-03-0099) under a grant agreement with the Research Council of Lithuania (LMTLT), to AB; and the Project ThinkGut (EFA345/19), 65% co-financed by the European Regional Development Fund (ERDF) through the Interreg V-A Spain-France-Andorra programme (POCTEFA 2014-2020)

The establishment of the gut microbiota poses implications for short and long-term health. Bifidobacterium is an important taxon in early life, being one of the most abundant genera in the infant intestinal microbiota and carrying out key functions for maintaining host-homeostasis. Recent metagenomic studies have shown that different factors, such as gestational age, delivery mode, or feeding habits, affect the gut microbiota establishment at high phylogenetic levels. However, their impact on the specific bifidobacterial populations is not yet well understood. Here we studied the impact of these factors on the different Bifidobacterium species and subspecies at both the quantitative and qualitative levels. Fecal samples were taken from 85 neonates at 2, 10, 30, 90 days of life, and the relative proportions of the different bifidobacterial populations were assessed by 16S rRNA–23S rRNA internal transcribed spacer (ITS) region sequencing. Absolute levels of the main species were determined by q-PCR. Our results showed that the bifidobacterial population establishment is affected by gestational age, delivery mode, and infant feeding, as it is evidenced by qualitative and quantitative changes. These data underline the need for understanding the impact of perinatal factors on the gut microbiota also at low taxonomic levels, especially in the case of relevant microbial populations such as Bifidobacterium. The data obtained provide indications for the selection of the species best suited for the development of bifidobacteria-based products for different groups of neonates and will help to develop rational strategies for favoring a healthy early microbiota development when this process is challenged., This work was funded by the EU Joint Programming Initiative—A Healthy Diet for a Healthy Life (JPI HDHL, http://www.healthydietforhealthylife.eu/, Project EarlyMicroHealth) and the Project AGL2017-83653R funded by the Spanish “Ministerio de Ciencia, Innovación y Universidades (MCIU), Agencia Estatal de Investigación (AEI) and FEDER”. S.A. was the recipient of a Juan de la Cierva Postdoctoral Contract (Ministry of Science, Innovation, and Universities, Ref. IJCI-2017-32156) and an EU Horizon2020 research grant under the Marie Sklodowska-Curie program (n. 749255).

The genus Bifidobacterium constitutes one of the main groups of the human microbiota and some species have a long history of safe consumption supporting an excellent safety record. However, in the context of the increasing worldwide problems associate to the rise of pathogenic microorganisms with acquired resistance to antibiotics, the risk associated to the presence of antibiotic resistance determinants should always be a key starting point for the introduction of any microbial strain into the food chain. Bifidobacteria are not an exception and the presence of resistance to antibiotics is of interest since these microorganisms could potentially act as a reservoir of such resistances. In this context it is necessary to evaluate the presence of antibiotic resistance in any bifidobacterial strain to be included into the food chain. To this end, the first step is the determination of the antibiotic resistance pattern of the strain and the comparison with the susceptibility breakpoints for that species, allowing identifying the presence of atypical resistances in the strain. In this chapter we discuss the many efforts done to harmonize the methods used for the evaluation of antimicrobial susceptibility in the genus Bifidobacterium and the currently available guidelines. Moreover, we describe, in detail, the reference protocols used for evaluating the in vitro antimicrobial activity on bifidobacteria.

Ensuring the nutritional demands of preterm (PT) infants during complementary feeding could contribute significantly to the infants’ long-term health and development. However, the dietary guidelines for complementary feeding in PT are scarce. Thus, describing dietary intake and identifying nutritional targets for these infants could be of great interest. The aim of this study is to assess the food intake and anthropometric parameters in a Mediterranean infant cohort from 6 to 24 months and to identify nutritional targets especially focused on late preterm infants. This is a longitudinal prospective study analyzing information from administered questionnaires about general characteristics and food frequency consumption in 115 infants (20 PT (32 to 36 gestational weeks), 95 full-term (FT)) at 6, 12 and 24 months of age. Results show that the differences in the prevalence of underweight observed in PT infants vs. FT infants are maintained for up to 6 months of age but disappear at 12 and 24 months. The age of inclusion of new foods and the average intake of the main food groups was not different from that of FTs. Although protein intake at 6 months was directly correlated with weight gain and growth in FT, these associations were not observed in PT. At the nutritional level, the low intake of vitamin D in preterm infants is noteworthy. These findings may be useful when designing new intervention strategies for this population group., This work was financed by PCIN-2015-233 (Project EarlyMicroHealth from the EU Joint Program Initiative HDHL) (MINECO/FEDER, UE) and by the University of Oviedo (Diet, Rhythms and Early Acquisition Microbiota (DREAMS) Project, REF. 2017/00001/003/005/013). Silvia Arboleya is the recipient of a Juan de la Cierva postdoctoral contract from the Spanish Ministry of Science and Innovation (Ref. IJCI-2017-32156) and María Gómez-Martín is the recipient of a predoctoral FPU contract (FPU18/03393) funded by the Spanish Ministry of Science, Innovation and Universities.

The early life gut microbiota has been reported to be involved in neonatal weight gain and later infant growth. Therefore, this early microbiota may constitute a target for the promotion of healthy neonatal growth and development with potential consequences for later life. Unfortunately, we are still far from understanding the association between neonatal microbiota and weight gain and growth. In this context, we evaluated the relationship between early microbiota and weight in a cohort of full-term infants. The absolute levels of specific fecal microorganisms were determined in 88 vaginally delivered and 36 C-section-delivered full-term newborns at 1 month of age and their growth up to 12 months of age. We observed statistically significant associations between the levels of some early life gut microbes and infant weight gain during the first year of life. Classifying the infants into tertiles according to their Staphylococcus levels at 1 month of age allowed us to observe a significantly lower weight at 12 months of life in the C-section-delivered infants from the highest tertile. Univariate and multivariate models pointed out associations between the levels of some fecal microorganisms at 1 month of age and weight gain at 6 and 12 months. Interestingly, these associations were different in vaginally and C-section-delivered babies. A significant direct association between Staphylococcus and weight gain at 1 month of life was observed in vaginally delivered babies, whereas in C-section-delivered infants, lower Bacteroides levels at 1 month were associated with higher later weight gain (at 6 and 12 months). Our results indicate an association between the gut microbiota and weight gain in early life and highlight potential microbial predictors for later weight gain., This work was funded by the EU Joint Programming Initiative—A Healthy Diet for a Healthy Life (JPI HDHL. http://www.healthydietforhealthylife.eu/; accessed on 14 July 2021. Project EarlyMicroHealth) and the Project AGL2017-83653R funded by the Spanish “Ministerio de Ciencia, Innovación y Universidades (MCIU), Agencia Estatal de Investigación (AEI) and FEDER” and by the European Research Council under the European Union’s Horizon 2020 research and innovation program (ERC starting grant, no. 639226). Silvia Arboleya is the recipient of a Juan de la Cierva Postdoctoral Contract from the Spanish Ministry of Science and Innovation (Ref. IJCI-2017-32156) funded by the Spanish Ministry of Science, Innovation and Universities.

© 2020 by the authors., Choline is a water-soluble nutrient essential for human life. Gut microbial metabolism of choline results in the production of trimethylamine (TMA), which, upon absorption by the host is converted into trimethylamine-N-oxide (TMAO) in the liver. A high accumulation of both components is related to cardiovascular disease, inflammatory bowel disease, non-alcoholic fatty liver disease, and chronic kidney disease. However, the relationship between the microbiota production of these components and its impact on these diseases still remains unknown. In this review, we will address which microbes contribute to TMA production in the human gut, the extent to which host factors (e.g., the genotype) and diet affect TMA production, and the colonization of these microbes and the reversal of dysbiosis as a therapy for these diseases., This work was supported by the Ministry of Science, Innovation and Universities (PSI2017-83893-R to J.L.A.) and the Ministry of Economy and Business (PSI2015-73111-EXP to J.L.A., PSI2017-90806-REDT to J.L.A. and AGL2017-83653R to M.G.) (Spain). S.A. was the recipient of a postdoctoral Juan de la Cierva Contract (Ministry of Science, Innovation and Universities, Ref. IJCI-2017-32156).

The colonization of the neonatal digestive tract provides a microbial stimulus required for an adequate maturation towards the physiological homeostasis of the host. This colonization, which is affected by several factors, begins with facultative anaerobes and continues with anaerobic genera. Accumulating evidence underlines the key role of the early neonatal period for this microbiota-induced maturation, being a key determinant factor for later health. Therefore, understanding the factors that determine the establishment of the microbiota in the infant is of critical importance. Exposure to antibiotics, either prenatally or postnatally, is common in early life mainly due to the use of intrapartum prophylaxis or to the administration of antibiotics in C-section deliveries. However, we are still far from understanding the impact of early antibiotics and their long-term effects. Increased risk of non-communicable diseases, such as allergies or obesity, has been observed in individuals exposed to antibiotics during early infancy. Moreover, the impact of antibiotics on the establishment of the infant gut resistome, and on the role of the microbiota as a reservoir of resistance genes, should be evaluated in the context of the problems associated with the increasing number of antibiotic resistant pathogenic strains. In this article, we review and discuss the above-mentioned issues with the aim of encouraging debate on the actions needed for understanding the impact of early life antibiotics upon human microbiota and health and for developing strategies aimed at minimizing this impact., The work carried out in the authors’ laboratories on the early life microbiota is founded by the EU Joint Programming Initiative—A Healthy Diet for a Healthy Life (JPI HDHL, http://www.healthydietforhealthylife.eu/) and the Spanish Ministry of Economy and Competitiveness (MINECO) (Project EarlyMicroHealth). The Grant GRUPIN14-043 from “Plan Regional de Investigación del Principado de Asturias” is also acknowledged. A. M. N. is the recipient of a JPI predoctoral fellowship and N. S. benefits from a JdC contract, from the Spanish Ministry of Economy and Competitiveness (MINECO).

The gastrointestinal microbiota is emerging as a unique and inexhaustible source for metabolites with potential to modulate G-protein coupled receptors (GPCRs). The ghrelin receptor [growth hormone secretagogue receptor (GHSR)-1a] is a GPCR expressed throughout both the gut and the brain and plays a crucial role in maintaining energy balance,metabolism, and the centralmodulation of food intake,motivation, reward, andmood. To date, few studies have investigated the potential of the gastrointestinal microbiota and its metabolites to modulate GPCR signaling. Here we investigate the ability of short-chain fatty acids (SCFAs), lactate, and different bacterial strains, including Bifidobacteriumand Lactobacillus genera, tomodulateGHSR-1a signaling.We identify, forwhat is to our knowledge the first time, a potent effect ofmicrobiota-derivedmetabolites on GHSR-1a signaling with potential significant consequences for host metabolism and physiology. We show that SCFAs, lactate, and bacterial supernatants are able to attenuate ghrelin-mediated signaling through the GHSR-1a.We suggest a novel route of communication between the gut microbiota and the host via modulation of GHSR-1a receptor signaling. Together, this highlights the emerging therapeutic potential in the exploration of themicrobiota metabolome in the specific targeting of key GPCRs, with pleiotropic actions that span both the CNS and periphery., This study was supported by Science Foundation Ireland Research Centre Grant SFI/12/RC/2273 to the Alimentary Pharmabiotic Centre (APC) Microbiome Ireland, Student/Faculty Interaction (SFI) Grant 12/RC/2276 DBP and APC Microbiome Ireland industry partner Cremo SA

Non-alcoholic steatohepatitis (NASH) is one of the most prevalent diseases worldwide. While it has been suggested to cause nervous impairment, its neurophysiological basis remains unknown. Therefore, the aim of this study is to unravel the effects of NASH, through the interrelationship of liver, gut microbiota, and nervous system, on the brain and human behavior. To this end, 40 Sprague-Dawley rats were divided into a control group that received normal chow and a NASH group that received a high-fat, high-cholesterol diet. Our results show that 14 weeks of the high-fat, high-cholesterol diet induced clinical conditions such as NASH, including steatosis and increased levels of ammonia. Rats in the NASH group also demonstrated evidence of gut dysbiosis and decreased levels of short-chain fatty acids in the gut. This may explain the deficits in cognitive ability observed in the NASH group, including their depressive-like behavior and short-term memory impairment characterized in part by deficits in social recognition and prefrontal cortex-dependent spatial working memory. We also reported the impact of this NASH-like condition on metabolic and functional processes. Brain tissue demonstrated lower levels of metabolic brain activity in the prefrontal cortex, thalamus, hippocampus, amygdala, and mammillary bodies, accompanied by a decrease in dopamine levels in the prefrontal cortex and cerebellum and a decrease in noradrenalin in the striatum. In this article, we emphasize the important role of ammonia and gut-derived bacterial toxins in liver-gut-brain neurodegeneration and discuss the metabolic and functional brain regional deficits and behavioral impairments in NASH., This work was supported by the Ministry of Science, Innovation and Universities (PSI2017-83893-R to JLA) and the Ministry of Economy and Business (PSI2015-63658-R, PSI2015-73111-EXP to JLA, and PSI2017-90806-REDT to JLA) (Spain).

The fecal microbiota plays an important role in human health, and alterations in the microbiota&ndash, host interaction seem to be involved in the ageing process. Therefore, it is of interest to develop strategies for promoting a balanced microbiota in old age in order to prevent the physiological and immune decline associated with age. However, the specific microbiota changes in the transition from adulthood to senescence are not yet well understood. Here we assessed the levels of some intestinal microorganisms and short chain fatty acids (SCFAs) across different age-groups. In total, 153 adults from four age groups (&lt, 50, 50&ndash, 65, 66&ndash, 80, and &gt, 80 years-old) were recruited, the levels of different bacterial groups in fecal samples were determined by quantitative polymerase chain reaction (qPCR), and those of SCFA by gas chromatography. Dietary information was collected by using a Food Frequency Questionnaire. The presence of the Bifidobacterium, Faecalibacterium, Bacteroides group, and Clostridium cluster XIVa decreased with age up to 66&ndash, 80 years of age, with differences reaching statistical significance for the latter group. Interestingly, the levels of some of these microorganisms recovered in the very old age group (&gt, 80 years), with these older individuals presenting significantly higher counts of Akkermansia and Lactobacillus group than adults and the younger elderly. In addition, ageing was associated with a progressively and statistically significant reduction in the fecal concentrations of SCFAs. Dietary intakes also showed some statistically significant differences among the groups for some macro- and micronutrients. Moreover, associations of some microorganisms with age and macronutrients were also evidenced. Considering the role that fecal microbiota alterations may have in terms of impairing homeostasis and resilience, our results underline the importance of understanding the ageing and immunosenescence processes by including the microbiota perspective.

The gut microbiota remains relatively stable during adulthood; however, certain intrinsic and environmental factors can lead to microbiota dysbiosis. Its restoration towards a healthy condition using best-suited prebiotics requires previous development of in vitro models for evaluating their functionality. Herein, we carried out fecal cultures with microbiota from healthy normal-weight and morbid obese adults. Cultures were supplemented with different inulin-type fructans (1-kestose, Actilight, P95, Synergy1 and Inulin) and a galactooligosaccharide. Their impact on the gut microbiota was assessed by monitoring gas production and evaluating changes in the microbiota composition (qPCR and 16S rRNA gene profiling) and metabolic activity (gas chromatography). Additionally, the effect on the bifidobacterial species was assessed (ITS-sequencing). Moreover, the functionality of the microbiota before and after prebiotic-modulation was determined in an in vitro model of interaction with an intestinal cell line. In general, 1-kestose was the compound showing the largest effects. The modulation with prebiotics led to significant increases in the Bacteroides group and Faecalibacterium in obese subjects, whereas in normal-weight individuals, substantial rises in Bifidobacterium and Faecalibacterium were appreciated. Notably, the results obtained showed differences in the responses among the tested compounds but also among the studied human populations, indicating the need for developing population-specific products., The present work was financed by the project AGL2013-43770-R (receiving funds from the Ministry of Economy and Competitiveness—MINECO and the European Union FEDER funds) and by a contract with the company β- Food Sciences (Chita, Japan). Alicja M Nogacka was the recipient of a predoctoral contract granted by MINECO (reference BES-2014-068796), and S.A. received a postdoctoral Juan de la Cierva contract (Ministry of Science, Innovation and Universities, Spain, Ref. IJCI-2017-32156). Nuria Salazar is the recipient of a postdoctoral contract awarded by the Biosanitary Research Foundation in Asturias (FINBA, Spain)

The intestinal microbiota plays a key role in the maintenance of human health. Alterations in this microbiota have been described in several autoimmune diseases, including nervous system diseases. Nevertheless, the information regarding neuromuscular conditions is still limited. In this study, we aimed at characterizing the intestinal microbiota composition in myasthenia gravis patients (MG). To this end fecal samples were taken from ten patients, with antibodies against the acetylcholine receptor, and ten age and sex matched controls from the same population (Asturias region, Spain). Fecal samples were submitted to microbiota analyses by 16S rRNA gene profiling, bifidobacterial ITS-region profiling and qPCR. The fecal levels of short chain fatty acids were determined by gas chromatography. MG patients were found to harbor lower relative proportions of Verrucomicrobiaceae and Bifidobacteriaceae, among others, and increased of the phylum Bacteroidetes and the family Desulfovibrionaceae. The increase of these latter microbial groups was also confirmed at quantitative level by qPCR. In contrast, no statistically significant differences were found between MG patients and the control group in the bifidobacterial population at the species level or in short chain fatty acids profiles. Our data indicates an altered fecal microbiota pattern in MG patients and point out at specific microbiota targets for intervention in this population., This work was financed by projects AGL2017-83653R from Plan Estatal de I + D + I (Spanish Ministry of Economy and Competitiveness), and by Grant GRUPIN14-043 from Plan Regional de Investigación del Principado de Asturias, Spain. Both national and regional grants received cofounding from the European Union FEDER funds. SA is the recipient of a postdoctoral Marie Curie contract funded by the EU.

[Background]: The human gut microbiota is assembled during infancy with an increase in diversity and stability. The correct colonization and the establishment of this microbiome are linked to the early and future health status of the individual. It is known that caesarean delivery alters this optimal microbial foundation. C-section (CS) is a common obstetrician surgery; however, it is not without risk for the mother/infant dyad. The World Health Organization recommends not exceeding 10–15% of the total deliveries; nevertheless, this rate has been increasing rapidly worldwide in the last decades. [Summary]: This review discloses the clinical parameters for correct CS recommendation. Moreover, the major microbial changes in the infant gut microbiome acquisition as a consequence of delivery mode and medical practices surrounding it, as well as, the early and long-lasting effects for both mother and babies are discussed. In addition, some strategies for the gut microbiota restoration are analysed. The aim of this review is to show the need for the development of strategies for minimizing or limiting the impact of caesarean on the microbiome development, favouring future health., This work was financed by the EU Joint Programming Initiative – A Healthy Diet for a Healthy Life (JPI HDHL, http://www.healthydietforhealthylife.eu/) and the Spanish Ministry of Economy and Competitiveness (MINECO; Project EarlyMicroHealth), and by project AGL2017–83653R from Plan Estatal de I+D+I (Spanish Ministry of Economy and Competitiveness). S.A. is the recipient of a postdoctoral Marie-Curie contract funded by the E.U.

Background Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. Results We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). Conclusions The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome., This work was supported by The APC Microbiome Institute (under Science Foundation Ireland [SFI] grant number: SFI/12/RC/2273) and by Department of Agriculture Food and Marine (DAFM) funded INFANTMET (Infant Nutrition for Programming the Gut Microbiota in Neonates) Project (Ref No. 10FDairy).

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease., This work was funded by the EU Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL, http://www.healthydietforhealthylife.eu/) and MIUR to M.V. and by the Spanish MINECO to M.G. (project PCIN-2015-233). A.M. and S.D.P. are partially funded by grants from the Instituto Danone and by the Spanish Plan Estatal de I+D+I (reference AGL2016-78311-R). D.V.S. is a member of the APC Microbiome Institute funded by Science Foundation Ireland (SFI) through the Irish Government's National Development Plan (grant number SFI/12/RC/2273). J.M.R. is in receipt of AGL2016-75476-R (Ministerio de Economía y Competitividad (Spain). J.M. is in receipt of a Starting Investigator Research Grant (SIRG) (no. 15/SIRG/3430) funded by Science Foundation Ireland (SFI).

The colonisation and establishment of the intestinal microbiota starts immediately at birth and is essential for the development of the intestine and the immune system. This microbial community gradually increases in number and diversity until the age of two or three years when it becomes a stable ecosystem resembling that of adults. This period constitutes a unique window of opportunity to modulate it through probiotic action, with a potential impact in later health. In the present work we have investigated how putative bifidobacterial probiotics modify the metabolic profiles and immune-modulatory properties of faecal microbiotas. An in vitro pH-controlled single-stage continuous-culture system (CCS) inoculated with infant faeces was employed to characterise the effects of two Bifidobacterium species on the intestinal microbiotas in three children, together with the effects of these modified microbiotas on cytokine production by HT-29 cells. Intestinal bacterial communities, production of short-chain fatty acids and lactate were determined by quantitative PCR and gas chromatography, respectively. Cytokines production by HT-29 cells was measured by ELISA. The combination of CCS with infant faeces and human intestinal cells provided a suitable model to evaluate the specific modulation of the intestinal microbiota and immune system by probiotics. In the CCS, infant faecal microbiotas were influenced by the addition of bifidobacteria, resulting in changes in their ability to induce the production of immune mediators by HT-29 cells. The different metabolic and immunological responses induced by the bifidobacterial species tested indicate the need to assess potential probiotics in model systems including complex intestinal microbiotas. Potential probiotic bifidobacteria can modulate the infant microbiota and its ability to induce the production of mediators of the immune response by intestinal cells. © 2015 Wageningen Academic Publishers.

[Background]: Disturbances in the early establishment of the intestinal microbiota may produce important implications for the infant’s health and for the risk of disease later on. Different perinatal conditions may be affecting the development of the gut microbiota. Some of them, such as delivery mode or feeding habits, have been extensively assessed whereas others remain to be studied, being critical to identify their impact on the microbiota and, if any, to minimize it. Antibiotics are among the drugs most frequently used in early life, the use of intrapartum antimicrobial prophylaxis (IAP), present in over 30% of deliveries, being the most frequent source of exposure. However, our knowledge on the effects of IAP on the microbiota establishment is still limited. The aim of the present work was to evaluate the impact of IAP investigating a cohort of 40 full-term vaginally delivered infants born after an uncomplicated pregnancy, 18 of which were born from mothers receiving IAP., [Results]: Fecal samples were collected at 2, 10, 30, and 90 days of age. We analyzed the composition of the fecal microbiota during the first 3 months of life by 16S rRNA gene sequencing and quantified fecal short chain fatty acids by gas chromatography. The presence of genes for resistance to antibiotics was determined by PCR in the samples from 1-month-old infants. Our results showed an altered pattern of intestinal microbiota establishment in IAP infants during the first weeks of life, with lower relative proportions of Actinobacteria and Bacteroidetes and increased of Preoteobacteria and Firmicutes. A delay in the increase on the levels of acetate was observed in IAP infants. The analyses of specific antibiotic resistance genes showed a higher occurrence of some β-lactamase coding genes in infants whose mothers received IAP., [Conclusions]: Our results indicate an effect of IAP on the establishing early microbiota during the first months of life, which represent a key moment for the development of the microbiota-induced host homeostasis. Understanding the impact of IAP in the gut microbiota development is essential for developing treatments to minimize it, favoring a proper gut microbiota development in IAP-exposed neonates., This work was founded by the EU Joint Programming Initiative—A Healthy Diet for a Healthy Life (JPI HDHL, http://www.healthydietforhealthylife.eu/) as well as the Spanish Ministry of Economy and Competitiveness (MINECO) (Project “EarlyMicroHealth” PCIN-2015-233 and Project AGL2013-43770R), and Italian Ministry of Education, University and Research (MIUR) grant to MV and CM. A. Nogacka was the recipient of a FPI contract from MINECO, and NS benefits from a postdoctoral “Juan de la Cierva-Incorporación” grant from MINECO. The Grant GRUPIN14–043 from “Plan Regional de Investigación del Principado de Asturias” is also acknowledged., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

Microbial colonization of the infant gut is essential for the development of the intestine and the immune system. The intestinal microbiota of full-term breast-fed infants is considered as the health standard for newborns. A culture medium containing formula milk was designed, which allowed a balanced growth of intestinal microorganisms and was used to perform fecal batch cultures from preterm babies. Sixteen Bifidobacterium strains and fructooligosaccharides (FOS) were tested for their ability to modulate in vitro the intestinal microbiota. The production of short chain fatty acids (SCFA) was measured by Gas Chromatography and the levels of some anaerobe (Bifidobacterium and Bacteroides groups) and facultative anaerobes (Enterobacteriaceae, Enterococcaceae, Weissella group, and Klebsiella pneumoniae) were determined by quantitative PCR. Results were referred to a fecal negative control culture without microorganisms or FOS added. Strains that in fecal cultures counteracted better the aberrancies previously found in feces of preterm babies, as compared with full-term breast-fed infants, were selected. The three Bifidobacterium bifidum strains tested in this work promoted the most suitable shifts in SCFA and in the ratio of variables facultative anaerobes to anaerobes. Two Bifidobacterium breve strains complied with the requirement for facultative anaerobes and anaerobes and one of them also promoted a suitable shift of SCFA. Bifidobacteria behaved similarly as FOS regarding the microbial profiles in fecal cultures but the production of lactic and acetic acid was much lower. B. breve and B. bifidum strains selected represent promising candidates for their assessment in more complex in vitro and in vivo models. © 2012 Elsevier Ltd., This work was financially supported by a Spanish Ministry of Science and Innovation (MICINN) project (AGL2010-16525) and by a CSIC intramural project (Ref. 200870I049).

During recent years there has been an increasing interest on the development of strategies for modulating the process of microbiota establishment in preterm infants. For successfully developing of such strategies, a detailed knowledge of the microbiota establishment process in these infants is needed. In a previous study we evidenced clear alterations in the process of microbiota establishment in preterm newborns when compared with a control group of full-term breast-fed infants. Here we have analyzed these data more in depth, corroborating a reduced proportion of strict anaerobes with respect to facultatives in the fecal microbiota of preterm infants. The potential benefits, as well as the side effects, of strategies aimed at counterbalancing this alteration in the facultative to strict anaerobes ratio are discussed in this addendum. © 2012 Landes Bioscience.

[Background] The microbial colonization of the neonatal gut provides a critical stimulus for normal maturation and development. This process of early microbiota establishment, known to be affected by several factors, constitutes an important determinant for later health., [Methods] We studied the establishment of the microbiota in preterm and full-term infants and the impact of perinatal antibiotics upon this process in premature babies. To this end, 16S rRNA gene sequence-based microbiota assessment was performed at phylum level and functional inference analyses were conducted. Moreover, the levels of the main intestinal microbial metabolites, the short-chain fatty acids (SCFA) acetate, propionate and butyrate, were measured by Gas-Chromatography Flame ionization/Mass spectrometry detection., [Results] Prematurity affects microbiota composition at phylum level, leading to increases of Proteobacteria and reduction of other intestinal microorganisms. Perinatal antibiotic use further affected the microbiota of the preterm infant. These changes involved a concomitant alteration in the levels of intestinal SCFA. Moreover, functional inference analyses allowed for identifying metabolic pathways potentially affected by prematurity and perinatal antibiotics use., [Conclusion] A deficiency or delay in the establishment of normal microbiota function seems to be present in preterm infants. Perinatal antibiotic use, such as intrapartum prophylaxis, affected the early life microbiota establishment in preterm newborns, which may have consequences for later health., This work was founded by the EU Joint Programming Initiative–A Healthy Diet for a Healthy Life (JPI HDHL, http://www.healthydietforhealthylife.eu/) and the Spanish Ministry of Economy and Competitiveness (MINECO) (Project EarlyMicroHealth). Borja Sánchez was the recipient of a Ramón y Cajal Postdoctoral contract (RYC-2012-10052) from MINECO. The Grant GRUPIN14-043 from “Plan Regional de Investigación del Principado de Asturias” is also acknowledged., We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).

The intestinal microbiota is a complex community that plays an important role in human health from the initial steps of its establishment. Its microbial composition has been suggested to result from selective pressures imposed by the host and is modulated by competition among its members. Bifidobacterium longum is one of the most abundant species of the Bifidobacterium genus in the gut microbiota of healthy breast-fed infants and adults. The recent advancements of ‘omics techniques have facilitated the genetic and functional studies of different gut microbiota members. They have revealed the complex genetic pathways used to metabolize different compounds that likely contribute to the competitiveness and persistence of B. longum in the colon. The discovery of a genomic island in B. longum ssp. infantis that encodes specific enzymes for the metabolism of human milk oligosaccharides suggests a specific ecological adaptation. Moreover, B. longum is widely used as probiotic, and beneficial effects in infant health have been reported in several studies.

Special issue: 3rd International Symposium on Propionibacteria and Bifidobacteria: Dairy and Probiotic applications, Oviedo 1-4 June 2010., Most of the current commercial probiotic strains have not been selected for specific applications, but rather on the basis of their technological potential for use in diverse applications. Therefore, by selecting them from appropriate sources, depending on the target population, it is likely that better performing strains may be identified. Few strains have been specifically selected for human neonates, where the applications of probiotics may have a great positive impact. Breast-milk constitutes an interesting source of potentially probiotic bifidobacteria for inclusion in infant formulas and foods targeted to both pre-term and full-term infants. In this study six Bifidobacterium strains isolated from breast-milk were phenotypically and genotypically characterised according to international guidelines for probiotics. In addition, different in vitro tests were used to assess the safety and probiotic potential of the strains. Although clinical data would be needed before drawing any conclusion on the probiotic properties of the strains, our results indicate that some of them may have probiotic potential for their inclusion in products targeting infants. © 2010 Elsevier B.V., This study was funded by projects PIE 200870I049 (CSIC) and RM2007-00003-00-00 (INIA). S. Arboleya was the recipient of a JAE predoctoral fellowship from CSIC.

Objectives To assess the establishment of the intestinal microbiota in very low birthweight preterm infants and to evaluate the impact of perinatal factors, such as delivery mode and perinatal antibiotics. Study design We used 16S ribosomal RNA gene sequence-based microbiota analysis and quantitative polymerase chain reaction to evaluate the establishment of the intestinal microbiota. We also evaluated factors affecting the microbiota, during the first 3 months of life in preterm infants (n = 27) compared with full-term babies (n = 13). Results Immaturity affects the microbiota as indicated by a reduced percentage of the family Bacteroidaceae during the first months of life and by a higher initial percentage of Lactobacillaceae in preterm infants compared with full term infants. Perinatal antibiotics, including intrapartum antimicrobial prophylaxis, affects the gut microbiota, as indicated by increased Enterobacteriaceae family organisms in the infants. Conclusions Prematurity and perinatal antibiotic administration strongly affect the initial establishment of microbiota with potential consequences for later health. © 2015 Elsevier Inc.

The use of beneficial microorganisms, the so-called probiotics, to improve human health is gaining popularity. However, not all of the probiotic strains trigger the same responses and they differ in their interaction with the host. In spite of the limited knowledge on mechanisms of action some of the probiotic effects seem to be exerted through maintenance of the gastrointestinal barrier function and modulation of the immune system. In the present work, we have addressed in vitro the response of the intestinal epithelial cell line HT29 to the strain Bifidobacterium breve IPLA20004. In the array of 84 genes involved in inflammation tested, the expression of 12 was modified by the bifidobacteria. The genes of chemokine CXCL6, the chemokine receptor CCR7, and, specially, the complement component C3 were upregulated. Indeed, HT29 cells cocultivated with B. breve produced significantly higher levels of protein C3a. The proteome of HT29 cells showed increased levels of cytokeratin-8 in the presence of B. breve. Altogether, it seems that B. breve IPLA20004 could favor the recruitment of innate immune cells to the mucosa reinforcing, as well as the physical barrier of the intestinal epithelium. © 2015 Borja Sánchez et al., This work was financed by Projects PIE201370E019 from CSIC and AGL2009-09445 and AGL2013-43770R from the Spanish “Ministerio de Economia y Competitividad” Silvia Arboleya was funded by a predoctoral JAE Fellowship from CSIC. Irene González-Rodríguez was the recipient of a FPI grant and Borja Sánchez of a Juan de la Cierva postdoctoral contract, both from the Spanish “Ministerio de Ciencia e Innovación.”

Metagenomic studies on the gut microbiota of preterm infants are scarce. We characterized the microbiota of 10 days-old neonates by deep 16S rRNA gene metagenomic analysis and compare the results with those obtained by qPCR. Both techniques lead to similar conclusions, allowing differentiating between preterm and full-term infants. © 2012 Elsevier Ltd., This work was funded by a CSIC (Spain) intramural project (Ref. 200870I049).

Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease in humans and is characterized by the presence of hyperactive immune cells and aberrant antibody responses to nuclear and cytoplasmic antigens, including characteristic anti–double-stranded DNA antibodies. We performed a cross-sectional study in order to determine if an SLE-associated gut dysbiosis exists in patients without active disease. A group of 20 SLE patients in remission, for which there was strict inclusion and exclusion criteria, was recruited, and we used an optimized Ion Torrent 16S rRNA gene-based analysis protocol to decipher the fecal microbial profiles of these patients and compare them with those of 20 age- and sex-matched healthy control subjects. We found diversity to be comparable based on Shannon’s index. However, we saw a significantly lower Firmicutes/Bacteroidetes ratio in SLE individuals (median ratio, 1.97) than in healthy subjects (median ratio, 4.86; P < 0.002). A lower Firmicutes/Bacteroidetes ratio in SLE individuals was corroborated by quantitative PCR analysis. Notably, a decrease of some Firmicutes families was also detected. This dysbiosis is reflected, based on in silico functional inference, in an overrepresentation of oxidative phosphorylation and glycan utilization pathways in SLE patient microbiota. IMPORTANCE: Growing evidence suggests that the gut microbiota might impact symptoms and progression of some autoimmune diseases. However, how and why this microbial community influences SLE remains to be elucidated. This is the first report describing an SLE-associated intestinal dysbiosis, and it contributes to the understanding of the interplay between the intestinal microbiota and the host in autoimmune disorders. © 2014 Hevia et al., This study was financed by European Union FEDER funds and the Spanish Plan Nacional de I+D (grant AGL2010-14952). Arancha Hevia was the recipient of an FPI grant, and Borja Sánchez was the recipient of a Juan de la Cierva postdoctoral contract, both from the Spanish Ministerio de Ciencia e Innovación.

The microbial colonisation of the infant gut begins immediately after birth and is essential for the development of the intestine, the immune system and later well-being. Important differences have been reported in the characteristics of such microbiota in different infant population groups. In the present study, we employed an in vitro faecal batch culture model using faeces from different human population groups (adults and full-term breast-fed, full-term formula-fed and preterm infants) to determine the influence that the addition of four bifidobacterial strains and fructo-oligosaccharides (FOS) exerts on the profile of SCFA measured by GC as well as on the levels of some relevant intestinal microbial groups by quantitative PCR during incubation. Differences were found in the levels of SCFA and intestinal microbial groups in the faecal cultures depending on the human group origin of the faecal samples (P

Microbial colonization of the infant gut is essential for the development of the intestine and the immune system. The profile of intestinal microbiota in the full-term, vaginally delivered, breast-fed infant is considered as ideally healthy. However, in preterm infants this process is challenging, mainly because of organ immaturity, antibiotics use, and hospital stay. To assist in a proper microbiota development in these infants, a detailed knowledge of the colonization process, and the differences from that of full-term breast-fed infants, is needed. We assessed the establishment of the gut microbiota and its metabolic activity in preterm neonates (n = 21) during the first 3 months of life and compared it with that of vaginally delivered, exclusively breast-fed full-term infants (n = 20) using qualitative and quantitative culture-independent methods. Differences in the gut microbiota composition between both groups were observed. Preterm infants showed higher levels of facultative anaerobic microorganisms and reduced levels of strict anaerobes such as Bifidobacterium, Bacteroides, and Atopobium. Short-chain fatty acids concentrations were lower in preterm infants during the first days of life. Alterations occur in the process of microbiota establishment in preterm infants, indicating the need for intervention strategies to counteract them. © 2011 Federation of European Microbiological Societies., This work was funded by a CSIC (Spain) intramural project (Ref. 200870I049). S.A. was funded by a predoctoral JAE fellowship from CSIC, Spain. A.B. was the recipient of a postdoctoral fellowship from CONICET, Argentina.