Why is initial bacterial colonization of the intestine important to infants' and children's health?

The association of maternal factors with the neonatal microbiota and health

The human microbiome plays a crucial role in human health. However, the influence of maternal factors on the neonatal microbiota remains obscure. Herein, our observations suggest that the neonatal microbiotas, particularly the buccal microbiota, change rapidly within 24-48 h of birth but begin to stabilize by 48-72 h after parturition. Network analysis clustered over 200 maternal factors into thirteen distinct groups, and most associated factors were in the same group. Multiple maternal factor groups were associated with the neonatal buccal, rectal, and stool microbiotas. Particularly, a higher maternal inflammatory state and a lower maternal socioeconomic position were associated with a higher alpha diversity of the neonatal buccal microbiota and beta diversity of the neonatal stool microbiota was influenced by maternal diet and cesarean section by 24-72 h postpartum. The risk of admission of a neonate to the newborn intensive care unit was associated with preterm birth as well as higher cytokine levels and probably higher alpha diversity of the maternal buccal microbiota.

Supplementing infant milk formula with a multi-strain synbiotic and osteopontin enhances colonic microbial colonization and modifies jejunal gene expression in lactating piglets

A total of ninety-six weaned piglets were assigned to four dietary treatments in a 2 × 2 design. The treatments included: a standard milk formula (CTR); CTR + probiotics (6.4 × 108 cfu L-1Bifidobacterium longum subsp. infantis CECT 7210 and 1.1 × 108 cfu L-1Lactobacillus rhamnosus NH001) + prebiotics (galacto-oligosaccharides 4.36 g L-1 and human-milk-oligosaccharide 0.54 g L-1) (SYN); CTR + osteopontin (0.43 g L-1) (OPN); and CTR + SYN + OPN (CON). Daily records including feed intake, body weight, and clinical signs, were maintained throughout the 15-day trial. At the end of the study samples from blood, digestive content, and gut tissues were collected to determine serum TNF-α, intestinal fermentative activity (SCFA and ammonia), colonic microbiota (16S rRNA Illumina-MiSeq), histomorphology, and jejunal gene expression (Open-Array). No statistical differences were found in weight gain; however, the animals supplemented with osteopontin exhibited higher feed intake. In terms of clinical signs, synbiotic supplementation led to a shorter duration of diarrhoea episodes. Regarding gut health, the sequenced faecal microbiota revealed better control of potentially dysbiotic bacteria with the CON diet at day 15. In the colon compartment, a significant increase in SCFA concentration, a decrease in ammonia concentration, and a significant decrease in intraepithelial lymphocyte counts were particularly observed in CON animals. The supplemented diets were also associated with modified jejunal gene expression. The synbiotic combination was characterized by the upregulation of genes related to intestinal maturation (ALPI, SI) and nutrient transport (SLC13A1, SLC15A1, SLC5A1, SLC7A8), and the downregulation of genes related to the response to pathogens (GBP1, IDO, TLR4) or the inflammatory response (IDO, IL-1β, TGF-β1). Osteopontin promoted the upregulation of a digestive function gene (GCG). Correlational analysis between the microbiota population and various intestinal environmental factors (SCFA concentration, histology, and gene expression) proposes mechanisms of communication between the gut microbiota and the host. In summary, these results suggest an improvement in the colonic colonization process and a better modulation of the immune response when milk formula is supplemented with the tested synbiotic combined with osteopontin, benefiting from a synergistic effect.

Contemporary use of prophylactic probiotics in NICUs in the United States: a survey update

OBJECTIVE

In 2015, 14.0% of US NICUs administered probiotics to very low birth weight infants. Current probiotic use prior to and after the Fall of 2023 (when FDA warnings were issued) remains unknown.

STUDY DESIGN

A survey was distributed to the American Academy of Pediatrics Section on Neonatal and Perinatal Medicine (August-November/2022) and Neonatology Solutions' Level III/IV NICUs (January-April/2023). Probiotic administration practices were investigated.

RESULTS

In total, 289 unique NICUs and 406 providers responded to the survey. Of those, 29.1% of NICUs administered prophylactic probiotics to premature neonates, however, this decreased considerably after FDA warnings were issued. Additionally, 71.4% of providers stated willingness to administer probiotics to premature infants if there was an FDA-approved formulation.

CONCLUSIONS

Probiotic use in US NICUs increased between 2015 and the Fall of 2023 and then dropped dramatically following warning letters from the FDA. The introduction of an FDA-approved probiotic may further expand administration.

Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance

BACKGROUND

Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers.

METHODS

A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens.

RESULTS

Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons.

CONCLUSIONS

The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.

A Murine Model of Maternal Micronutrient Deficiencies and Gut Inflammatory Host-microbe Interactions in the Offspring

BACKGROUND & AIMS

Micronutrient deficiency (MND) (ie, lack of vitamins and minerals) during pregnancy is a major public health concern. Historically, studies have considered micronutrients in isolation; however, MNDs rarely occur alone. The impact of co-occurring MNDs on public health, mainly in shaping mucosal colonization by pathobionts from the Enterobacteriaceae family, remains undetermined due to lack of relevant animal models.

METHODS

To establish a maternal murine model of multiple MND (MMND), we customized a diet deficient in vitamins (A, B12, and B9) and minerals (iron and zinc) that most commonly affect children and women of reproductive age. Thereafter, mucosal adherence by Enterobacteriaceae, the associated inflammatory markers, and proteomic profile of intestines were determined in the offspring of MMND mothers (hereafter, low micronutrient [LM] pups) via bacterial plating, flow cytometry, and mass spectrometry, respectively. For human validation, Enterobacteriaceae abundance, assessed via 16s sequencing of 3-month-old infant fecal samples (n = 100), was correlated with micronutrient metabolites using Spearman's correlation in meconium of children from the CHILD birth cohort.

RESULTS

We developed an MMND model and reported an increase in colonic abundance of Enterobacteriaceae in LM pups at weaning. Findings from CHILD cohort confirmed a negative correlation between Enterobacteriaceae and micronutrient availability. Furthermore, pro-inflammatory cytokines and increased infiltration of lymphocyte antigen 6 complex high monocytes and M1-like macrophages were evident in the colons of LM pups. Mechanistically, mitochondrial dysfunction marked by reduced expression of nicotinamide adenine dinucleotide (NAD)H dehydrogenase and increased expression of NAD phosphate oxidase (Nox) 1 contributed to the Enterobacteriaceae bloom.

CONCLUSION

This study establishes an early life MMND link to intestinal pathobiont colonization and mucosal inflammation via damaged mitochondria in the offspring.

A bacterial sensor taxonomy across earth ecosystems for machine learning applications

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.

Nerolidol attenuates airway inflammation and airway remodeling and alters gut microbes in ovalbumin-induced asthmatic mice

Asthma is a common respiratory disease associated with airway inflammation. Nerolidol is an acyclic sesquiterpenoid with anti-inflammatory properties. BALB/C mice were sensitized with ovalbumin (OVA) to induce asthma symptoms and given different doses of Nerolidol. We found that Nerolidol reduced OVA-induced inflammatory cell infiltration, the number of goblet cells and collagen deposition in lung tissue. Nerolidol reduced the OVA-specific IgE levels in serum and alveolar lavage fluid in an asthma model. Immunohistochemical staining of α-SMA (the marker of airway smooth muscle) showed that Nerolidol caused bronchial basement membrane thinning in asthmatic mice. The hyperplasia of airway smooth muscle cells (ASMCs) is an important feature of airway remodeling in asthma. ASMCs were treated with 10 ng/mL TGF-β to simulate the pathological environment of asthma in vitro and then treated with different doses of Nerolidol. Nerolidol inhibited the activity of TGF-β/Smad signaling pathway both in the lung tissue of OVA-induced mouse and TGF-β-stimulated ASMCs. 16s rRNA sequencing was performed on feces of normal mice, the changes of intestinal flora in OVA-induced asthmatic mice and Nerolidol-treated asthmatic mice were studied. The results showed that Nerolidol reversed the reduced gut microbial alpha diversity in asthmatic mice. Nerolidol changed the relative abundance of gut bacteria at different taxonomic levels. At the phylum level, the dominant bacteria were Bacteroidota, Firmicutes, and Proteobacteria. At the genus level, the dominant bacteria were Lactobacillus, Muribaculaceae, Bacteroides, and Lachnospiraceae. We conclude that Nerolidol attenuates OVA-induced airway inflammation and alters gut microbes in mice with asthma via TGF-β/Smad signaling.

Early life gut microbiome in children following spontaneous preterm birth and maternal preeclampsia

The early life microbiome plays an important role in developmental and long-term health outcomes. However, it is unknown whether adverse pregnancy complications affect the offspring's gut microbiome postnatally and in early years. In a longitudinal cohort with a five-year follow-up of mother-child pairs affected by preeclampsia (PE) or spontaneous preterm birth (sPTB), we evaluated offspring gut alpha and beta diversity as well as taxa abundances considering factors like breastfeeding and mode of delivery. Our study highlights a trend where microbiome diversity exhibits comparable development across adverse and normal pregnancies. However, specific taxa at genus level emerge with distinctive abundances, showing enrichment and/or depletion over time in relation to PE or sPTB. These findings underscore the potential for certain adverse pregnancy complications to induce alterations in the offspring's microbiome over the course of early life. The implications of these findings on the immediate and long-term health of offspring should be investigated in future studies.

Maternal transmission of bacterial microbiota during embryonic development in a viviparous lizard

IMPORTANCE

We investigated the presence and diversity of bacteria in the embryos of the viviparous lizard Sceloporus grammicus and their amniotic environment. We compared this diversity to that found in the maternal intestine, mouth, and cloaca. We detected bacterial DNA in the embryos, albeit with a lower bacterial species diversity than found in maternal tissues. Most of the bacterial species detected in the embryos were also found in the mother, although not all of them. Interestingly, we detected a high similarity in the composition of bacterial species among embryos from different mothers. These findings suggest that there may be a mechanism controlling the transmission of bacteria from the mother to the embryo. Our results highlight the possibility that the interaction between maternal bacteria and the embryo may affect the development of the lizards.

Gastroesophageal reflux and PPI exposure alter gut microbiota in very young infants

Importance

Infants with symptomatic Gastroesophageal reflux are treated with pharmacological therapy that includes proton pump inhibitors (PPI) with clinical improvement. The alterations to gut microbiome profiles in comparison to infants without reflux is not known.

Objective

To determine the effect of PPI therapy on gut bacterial richness, diversity, and proportions of specific taxa in infants when compared to infants not exposed to acid suppressive therapy.

Design setting and participants

This cohort study was conducted at the Stony Brook Hospital in Stony Brook, NY between February 2016, and June 2019. Infants meeting inclusion criteria were enrolled in a consecutive fashion.

Results

A total of 76 Infants were recruited and 60 were enrolled in the study, Twenty nine infants met clinical criteria for reflux and were treated with PPI therapy: median [IQR] gestation: 38.0 weeks [34.7-39.6 weeks]; median [IQR] birthweight: 2.95 Kg [2.2-3.4]; 14 [46.7%] male) and 29 infant were healthy controls median [IQR] gestation: 39.1 weeks [38-40 weeks]; median [IQR] birthweight: 3.3 Kg [2.2-3.4]; 17 [58.6%] male); 58 stool samples from 58 infants were analyzed. There were differences in Shannon diversity between the reflux and control groups. The reflux group that was exposed to PPI therapy had increased relative abundance of a diverse set of genera belonging to the phylum Firmicutes. On the other hand, the control group microbiota was dominated by Bifidobacterium, and a comparatively lower level of enrichment and abundance of microbial taxa was observed in this group of infants.

Conclusions and relevance

We observed significant differences in both α- and β-diversity of the microbiome, when the two groups of infants were compared. The microbiome in the reflux group had more bacterial taxa and the duration of PPIs exposure was clearly associated with the diversity and abundance of gut microbes. These findings suggest that PPI exposure among infants results in early enrichment of the intestinal microbiome.

Superior performance of biofilm versus planktonic Limosilactobacillus reuteri in protection of the intestines and brain in a piglet model of necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is the leading cause of gastrointestinal-related death in premature infants. Its etiology is multifactorial, with intestinal dysbiosis playing a major role. Probiotics are a logical preventative therapy for NEC, however their benefits have been inconsistent. We previously developed a novel probiotic delivery system in which planktonic (free-living) Limosilactobacillus reuteri (Lr) is incubated with biocompatible dextranomer microspheres (DM) loaded with maltose (Lr-DM-maltose) to induce biofilm formation. Here we have investigated the effects of Lr-DM-maltose in an enteral feed-only piglet model of NEC. We found a significant decrease in the incidence of Definitive NEC (D-NEC), death associated with D-NEC, and activated microglia in the brains of piglets treated with Lr-DM-maltose compared to non-treated piglets. Microbiome analyses using 16S rRNA sequencing of colonic contents revealed a significantly different microbial community composition between piglets treated with Lr-DM-maltose compared to non-treated piglets, with an increase in Lactobacillaceae and a decrease in Clostridiaceae in Lr-DM-maltose-treated piglets. Furthermore, there was a significant decrease in the incidence of D-NEC between piglets treated with Lr-DM-maltose compared to planktonic Lr. These findings validate our previous results in rodents, and support future clinical trials of Lr in its biofilm state for the prevention of NEC in premature neonates.

The preterm gut microbiota and administration routes of different probiotics: a randomized controlled trial

BACKGROUND

Preterm children with their aberrant gut microbiota and susceptibility to infections and inflammation constitute a considerable target group for probiotic therapy to generate the age-appropriate healthy microbiota.

METHODS

68 preterm neonates were randomized into five intervention groups: Beginning from the median age of 3 days, 13 children received Lactobacillus rhamnosus GG (LGG) directly orally, and 17 via the lactating mother. 14 children received LGG with Bifidobacterium lactis Bb-12 (Bb12) orally, and 10 via the lactating mother. 14 children received placebo. The children's faecal microbiota was assessed at the age of 7 days by 16S rRNA gene sequencing.

RESULTS

The gut microbiota compositions of the children directly receiving the probiotic combination (LGG + Bb12) were significantly different from those of the children receiving the other intervention modes or placebo (p = 0.0012; PERMANOVA), the distinction being due to an increase in the relative abundance of Bifidobacterium animalis (P < 0.00010; ANCOM-BC), and the order Lactobacillales (P = 0.020; ANCOM-BC).

CONCLUSION

The connection between aberrant primary gut microbiota and a heightened risk of infectious and non-communicable diseases invites effective microbiota modulation. We show that the direct, early, and brief probiotic intervention of LGG + Bb12 109 CFU each, is sufficient to modulate the gut microbiota of the preterm neonate.

IMPACT

Preterm children have a higher risk of several health problems partly due to their aberrant gut microbiota. More research is needed to find a safe probiotic intervention to modify the gut microbiota of preterm children. The maternal administration route via breast milk might be safer for the newborn. In our study, the early and direct administration of the probiotic combination Lactobacillus rhamnosus GG with Bifidobacterium lactis Bb-12 increased the proportion of bifidobacteria in the preterm children's gut at the age of 7 days, but the maternal administration route was not as effective.

The Sterilization of Human Milk by Holder Pasteurization or by High Hydrostatic Pressure Processing Leads to Differential Intestinal Effects in Mice

BACKGROUND

Human milk banks (HMBs) provide sterilized donor milk (DM) for the feeding of preterm infants. Most HMBs use the standard method of Holder pasteurization (HoP) performed by heating DM at 62.5 °C for 30 min. High hydrostatic pressure (HHP) processing has been proposed as an alternative to HoP. This study aims to evaluate intestinal barrier integrity and microbiota composition in adult mice subjected to a chronic oral administration of HoP- or HHP-DM.

METHODS

Mice were treated by daily gavages with HoP- or HHP-DM over seven days. Intestinal barrier integrity was assessed through in vivo 4 kDa FITC-dextran permeability assay and mRNA expression of several tight junctions and mucins in ileum and colon. Cecal short chain fatty acids (SCFAs) and microbiota were analyzed.

RESULTS

HHP-DM mice displayed decreased intestinal permeability to FITC-dextran and increased ileal mRNA expression levels of two tight junctions (Ocln and Cdh1) and Muc2. In the colon, mRNA expression levels of two tight junctions (Cdh1 and Tjp1) and of two mucins (Muc2 and Muc4) were decreased in HHP-DM mice. Cecal SCFAs and microbiota were not different between groups.

CONCLUSIONS

HHP processing of DM reinforces intestinal barrier integrity in vivo without affecting gut microbiota and SCFAs production. This study reinforces previous findings showing that DM sterilization through HHP might be beneficial for the intestinal maturation of preterm infants compared with the use of HoP for the treatment of DM.

Microbiome analysis of maternal and neonatal microbial communities associated with the different delivery modes based on 16S rRNA gene amplicon sequencing

OBJECTIVE

With the rising number of cases of non-vaginal delivery worldwide, scientists have been concerned about the influence of the different delivery modes on maternal and neonatal microbiomes. Although the birth rate trend is decreasing rapidly in Taiwan, more than 30 percent of newborns are delivered by caesarean section every year. However, it remains unclear whether the different delivery modes could have a certain impact on the postpartum maternal microbiome and whether it affects the mother-to-newborn vertical transmission of bacteria at birth.

MATERIALS AND METHODS

To address this, we recruited 30 mother-newborn pairs to participate in this study, including 23 pairs of vaginal delivery (VD) and seven pairs of caesarean section (CS). We here investigate the development of the maternal prenatal and postnatal microbiomes across multiple body habitats. Moreover, we also explore the early acquisition of neonatal gut microbiome through a vertical multi-body site microbiome analysis.

RESULTS AND CONCLUSION

The results indicate that no matter the delivery mode, it only slightly affects the maternal microbiome in multiple body habitats from pregnancy to postpartum. On the other hand, about 95% of species in the meconium microbiome were derived from one of the maternal body habitats; notably, the infants born by caesarean section acquire bacterial communities resembling their mother's oral microbiome. Consequently, the delivery modes play a crucial role in the initial colonization of the neonatal gut microbiome, potentially impacting children's health and development.

The tale of antibiotics beyond antimicrobials: Expanding horizons

Antibiotics had proved to be a godsend for mankind since their discovery. They were once the magical solution to the vexing problem of infection-related deaths. German scientist Paul Ehrlich had termed salvarsan as the silver bullet to treatsyphilis.As time passed, the magic of newly discovered silver bullets got tarnished with raging antibiotic resistance among bacteria and associated side-effects. Still, antibiotics remain the primary line of treatment for bacterial infections. Our understanding of their chemical and biological activities has increased immensely with advancement in the research field. Non-antibacterial effects of antibiotics are studied extensively to optimise their safer, broad-range use. These non-antibacterial effects could be both useful and harmful to us. Various researchers across the globe including our lab are studying the direct/indirect effects and molecular mechanisms behind these non-antibacterial effects of antibiotics. So, it is interesting for us to sum up the available literature. In this review, we have briefed the possible reason behind the non-antibacterial effects of antibiotics, owing to the endosymbiotic origin of host mitochondria. We further discuss the physiological and immunomodulatory effects of antibiotics. We then extend the review to discuss molecular mechanisms behind the plausible use of antibiotics as anticancer agents.

The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea

The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.

Metaanalyse zu präventiven und therapeutischen Effekten probiotischer Supplementierung bei Kindern mit atopischer Dermatitis

Trotz zahlreicher wissenschaftlicher Untersuchungen gibt es zur Wirkung von Probiotika auf die Inzidenz und Schwere der atopischen Dermatitis (AD) widersprüchliche Ergebnisse. Wir untersuchten, ob die Supplementierung mit Probiotika diese Parameter verringern. Dazu wurden drei Datenbanken systematisch durchsucht. In der Probiotika‐Gruppe war die AD‐Inzidenz um 22% geringer. Bei Verabreichung der Probiotika an schwangere und stillende Mütter betrug die Verringerung der Inzidenz 49% und bei Verabreichung an schwangere Mütter und Kinder 27%. Bei Verabreichung an schwangere und stillende Mütter sowie Kinder wurde eine 39%ige Verringerung der AD‐Inzidenz erreicht. Es wurden signifikante Unterschiede beim SCORAD (SCORing Atopic Dermatitis) zugunsten der Probiotika beobachtet, die IDLQI blieb jedoch unverändert. Lactobacillus (L.) rhamnosus war der am häufigsten dokumentierte Stamm, erwies sich jedoch bezüglich der Verringerung des SCORAD als unwirksam. Im Gegensatz dazu zeigte sich bei L. paracasei und L. sakei eine signifikante Verringerung des SCORAD. Während Probiotika bei der Prävention einer AD effektiv sind, ist die Wirkung bei der Behandlung einer AD weniger eindeutig, insbesondere bei Kindern <1 Jahr. Die Einnahme von Probiotika durch stillende Mütter ist eine wichtige Maßnahme und kann eine neue prophylaktische Strategie darstellen. Der präventive Effekt von Probiotika bei AD ist nicht mit dem familiären Hintergrund oder dem AD‐Risiko assoziiert. Bei L. paracasei und L. sakei zeigte sich die größte Verringerung des SCORAD.

Meta-analysis on preventive and therapeutic effects of probiotic supplementation in infant atopic dermatitis

Despite a large body of research, the effect of probiotic administration on the incidence and severity of atopic dermatitis (AD) shows conflicting results. We aimed to investigate whether probiotic supplementation reduces the incidence and severity of AD. Three databases were systematically searched. A 22% lower incidence of AD was found in the probiotic group. The reduction in incidence was 49% when probiotics were given to pregnant and lactating mothers, and 27% when they were given to pregnant mothers and infants. A 39% reduction of AD incidence was achieved when administered to pregnant-breastfeeding mothers and infants. Significant differences in SCORAD (SCORing Atopic Dermatitis) favoring probiotics were observed, but the IDLQI remained unchanged. Lactobacillus (L.) rhamnosus was the most documented strain, but it turned out to be ineffective in reducing SCORAD. Conversely, L. paracasei and L. sakei showed a significant decrease in SCORAD. Probiotics are effective in the prevention of AD, but the effect is less conclusive for the treatment of AD, especially in infants <1 year. The intake of probiotics by breastfeeding mothers is an important measure and may become a novel preventive strategy. The preventive effect of probiotics against AD is not associated with family background or AD risk. L. paracasei and L. sakei show the greatest reduction in SCORAD.

The Enzymatic Hydrolysis of Human Milk Oligosaccharides and Prebiotic Sugars from LAB Isolated from Breast Milk

Breastfeeding is essential in the first months of a newborn's life. Breast milk is a source of crucial macronutrients, prebiotic oligosaccharides, and potential probiotic strains of bacteria. Oligosaccharides from breast milk (HMOs) are a significant part of the composition of breast milk and represent a complex of digestible sugars. This study aims to elucidate the enzymatic hydrolysis of these oligosaccharides and other prebiotics by the bacteria present in breast milk. We used modified methods to isolate oligosaccharides (HMOs) from human milk. Using unique techniques, we isolated and identified different bacteria from breast milk, mainly Lactobacillus fermentum. Using enzymatic analyses, we established the participation of α-fucosidase, α-glucosidase, β-galactosidase, and β-glucosidase from breast milk bacteria in the hydrolysis of prebiotic sugars. We also optimized the scheme for isolating oligosaccharides from breast milk by putting the lyophilized product into different food media. We found that the oligosaccharides from breast milk (HMOs) are a potent inducer for the secretion of the studied bacterial enzymes. Also, we found that all the lactobacilli strains we studied in detail could digest mucin-linked glycans. The degradation of these sugars is perhaps a built-in defense mechanism in cases where other sugars are lacking in the environment. We also determined fucosidase activity in some of the isolated strains. We recorded the highest values (2.5 U/mg in L. fermentum ss8) when the medium's oligosaccharides isolated from breast milk were present. Lactobacilli and Bifidobacteria supplied with breast milk are the first colonizers in most cases in the gastrointestinal tract of the newborn. The presence and study of different genes for synthesizing other enzyme systems and transporters of various sugars in this type of bacteria are essential.

Genomic Characterisation of Multidrug-Resistant Pathogenic Enteric Bacteria from healthy children in Osun State, Nigeria

Antimicrobial resistance (AMR) has been established to be a significant driver for the persistence and spread of bacterial infections. It is, therefore, essential to conduct epidemiological surveillance of AMR in healthy individuals to understand the actual dynamics of AMR in Nigeria. Multi-drug resistant Klebsiella quasivariicola (n=1), Enterobacter hormaechei (n=1), and Escherichia coli (n=3) from stool samples of healthy children were subjected to whole genome sequencing using Illumina Nextseq1000/2000 and Oxford nanopore. Bioinformatics analysis reveals antimicrobial resistance, virulence genes, and plasmids. This pathogenic enteric bacteria harbored more than three plasmid replicons of either Col and/or Inc type associated with outbreaks and AMR resistant gene pmrB responsible for colistin resistance. Plasmid reconstruction revealed an integrated tetA gene responsible for tetracycline resistance, and caa gene responsible for toxin production in two of the E.coli isolates, and a cusC gene known to induce neonatal meningitis in the K. quasivariicola ST3879. The global spread of MDR pathogenic enteric bacteria is a worrying phenomenon, and close surveillance of healthy individuals, especially children, is strongly recommended to prevent the continuous spread and achieve the elimination and eradication of these infections. Molecular epidemiological surveillance using whole genome sequencing (WGS) will improve the detection of MDR pathogens in Nigeria.

Impact of Early Weaning on Development of the Swine Gut Microbiome

Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.

Whole-body microbiota of newborn calves and their response to prenatal vitamin and mineral supplementation

Early life microbial colonization and factors affecting colonization patterns are gaining interest due to recent developments suggesting that early life microbiome may play a role in Developmental Origins of Health and Disease. In cattle, limited information exists on the early microbial colonization of anatomical sites involved in bovine health beyond the gastrointestinal tract. Here, we investigated 1) the initial microbial colonization of seven different anatomical locations in newborn calves and 2) whether these early life microbial communities and 3) serum cytokine profiles are influenced by prenatal vitamin and mineral (VTM) supplementation. Samples were collected from the hoof, liver, lung, nasal cavity, eye, rumen (tissue and fluid), and vagina of beef calves that were born from dams that either received or did not receive VTM supplementation throughout gestation (n = 7/group). Calves were separated from dams immediately after birth and fed commercial colostrum and milk replacer until euthanasia at 30 h post-initial colostrum feeding. The microbiota of all samples was assessed using 16S rRNA gene sequencing and qPCR. Calf serum was subjected to multiplex quantification of 15 bovine cytokines and chemokines. Our results indicated that the hoof, eye, liver, lung, nasal cavity, and vagina of newborn calves were colonized by site-specific microbiota, whose community structure differed from the ruminal-associated communities (0.64 ≥ R² ≥ 0.12, p ≤ 0.003). The ruminal fluid microbial community was the only one that differed by treatment (p < 0.01). However, differences (p < 0.05) by treatment were detected in microbial richness (vagina); diversity (ruminal tissue, fluid, and eye); composition at the phylum and genus level (ruminal tissue, fluid, and vagina); and in total bacterial abundance (eye and vagina). From serum cytokines evaluated, concentration of chemokine IP-10 was greater (p = 0.02) in VTM calves compared to control calves. Overall, our results suggest that upon birth, the whole-body of newborn calves are colonized by relatively rich, diverse, and site-specific bacterial communities. Noticeable differences were observed in ruminal, vaginal, and ocular microbiota of newborn calves in response to prenatal VTM supplementation. These findings can derive future hypotheses regarding the initial microbial colonization of different body sites, and on maternal micronutrient consumption as a factor that may influence early life microbial colonization.

Probiotics and novel probiotic delivery systems

Necrotizing enterocolitis (NEC) is an infectious and inflammatory intestinal disease that is the most common surgical emergency in the premature patient population. Although the etiology of the disease is multifactorial, intestinal dysbiosis is a hallmark of this disease. Based on this, probiotics may play a therapeutic role in NEC by introducing beneficial bacteria with immunomodulating, antimicrobial, and anti-inflammatory functions into the gastrointestinal tract. Currently, there is no Food and Drug Administration (FDA)-approved probiotic for the prevention and treatment of NEC. All probiotic clinical studies to date have administered the bacteria in their planktonic (free-living) state. This review will discuss established probiotic delivery systems including planktonic probiotics, prebiotics, and synbiotics, as well as novel probiotic delivery systems such as biofilm-based and designer probiotics. We will also shed light on whether or not probiotic efficacy is influenced by administration with breast milk. Finally, we will consider the challenges associated with developing an FDA-approved probiotic for NEC.

Mechanistic Insights into Immune-Microbiota Interactions and Preventive Role of Probiotics Against Autoimmune Diabetes Mellitus

Recent studies on genetically susceptible individuals and animal models revealed the potential role of the intestinal microbiota in the pathogenesis of type 1 diabetes (T1D) through complex interactions with the immune system. T1D incidence has been increasing exponentially with modern lifestyle altering normal microbiota composition, causing dysbiosis characterized by an imbalance in the gut microbial community. Dysbiosis has been suggested to be a potential contributing factor in T1D. Moreover, several studies have shown the potential role of probiotics in regulating T1D through various mechanisms. Current T1D therapies target curative measures; however, preventive therapeutics are yet to be proven. This review highlights immune microbiota interaction and the immense role of probiotics and postbiotics as important immunological interventions for reducing the risk of T1D.

Gut microbiota and irritable bowel syndrome

Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that poses a significant health concern. Although its etiology remains unknown, there is growing evidence that gut dysbiosis is involved in the development and exacerbation of IBS. Previous studies have reported altered microbial diversity, abundance, and composition in IBS patients when compared to controls. However, whether dysbiosis or aberrant changes in the intestinal microbiota can be used as a hallmark of IBS remains inconclusive. We reviewed the literatures on changes in and roles of intestinal microbiota in relation to IBS and discussed various gut microbiota manipulation strategies. Gut microbiota may affect IBS development by regulating the mucosal immune system, brain-gut-microbiome interaction, and intestinal barrier function. The advent of high-throughput multi-omics provides important insights into the pathogenesis of IBS and promotes the development of individualized treatment for IBS. Despite advances in currently available microbiota-directed therapies, large-scale, well-organized, and long-term randomized controlled trials are highly warranted to assess their clinical effects. Overall, gut microbiota alterations play a critical role in the pathophysiology of IBS, and modulation of microbiota has a significant therapeutic potential that requires to be further verified.

Impact of the mother's gut microbiota on infant microbiome and brain development

The link between the gut microbiome and health has recently garnered considerable interest in its employment for medicinal purposes. Since the early microbiota exhibits more flexibility compared to that of adults, there is a considerable possibility that altering it will have significant consequences on human development. Like genetics, the human microbiota can be passed from mother to child. This provides information on early microbiota acquisition, future development, and prospective chances for intervention. The succession and acquisition of early-life microbiota, modifications of the maternal microbiota during pregnancy, delivery, and infancy, and new efforts to understand maternal-infant microbiota transmission are discussed in this article. We also examine the shaping of mother-to-infant microbial transmission, and we then explore possible paths for future research to advance our knowledge in this area.

A critical review of the recent concept of artificial mechanical uterus design in relation to the maternal microbiome: An Update to past researches

The microbiome in the female reproductive tract plays an essential role in immune modulation and reproductive health. However, various microbes become established during pregnancy, the balance of which plays a crucial role in embryonic development and healthy births. The contribution of disturbances in the microbiome profile to embryo health is poorly understood. A better understanding of the relationship between reproductive outcomes and the vaginal microbiota is needed to optimize the chances of healthy births. In this regards, microbiome dysbiosis refers to conditions in which the pathways of communication and balance within the normal microbiome are imbalanced due to the intrusion of pathogenic microorganisms into the reproductive system. This review summarizes the current state of knowledge on the natural human microbiome, with a focus on the natural uterine microbiome, mother-to-child transmission, dysbiosis, and the pattern of microbial change in pregnancy and parturition, and reviews the effects of artificial uterus probiotics during pregnancy. These effects can be studied in the sterile environment of an artificial uterus, and microbes with potential probiotic activity can be studied as a possible therapeutic approach. The artificial uterus is a technological device or biobag used as an incubator, allowing extracorporeal pregnancy. Establishing beneficial microbial communities within the artificial womb using probiotic species could modulate the immune system of both the fetus and the mother. The artificial womb could be used to select the best strains of probiotic species to fight infection with specific pathogens. Questions about the interactions and stability of the most appropriate probiotics, as well as dosage and duration of treatment, need to be answered before probiotics can be a clinical treatment in human pregnancy.

Molecular surveillance reveals widespread colonisation by carbapenemase and extended spectrum beta-lactamase producing organisms in neonatal units in Kenya and Nigeria

OBJECTIVES

Neonatal sepsis, a major cause of death amongst infants in sub-Saharan Africa, is often gut derived. Gut colonisation by Enterobacteriaceae producing extended spectrum beta-lactamase (ESBL) or carbapenemase enzymes can lead to antimicrobial-resistant (AMR) or untreatable infections. We sought to explore the rates of colonisation by ESBL or carbapenemase producers in two neonatal units (NNUs) in West and East Africa.

METHODS

Stool and rectal swab samples were taken at multiple timepoints from newborns admitted to the NNUs at the University College Hospital, Ibadan, Nigeria and the Jaramogi Oginga Odinga Teaching and Referral Hospital, Kisumu, western Kenya. Samples were tested for ESBL and carbapenemase genes using a previously validated qPCR assay. Kaplan-Meier survival analysis was used to examine colonisation rates at both sites.

RESULTS

In total 119 stool and rectal swab samples were taken from 42 infants admitted to the two NNUs. Colonisation with ESBL (37 infants, 89%) was more common than with carbapenemase producers (26, 62.4%; P = 0.093). Median survival time before colonisation with ESBL organisms was 7 days and with carbapenemase producers 16 days (P = 0.035). The majority of ESBL genes detected belonged to the CTX-M-1 (36/38; 95%), and CTX-M-9 (2/36; 5%) groups, and the most prevalent carbapenemase was bla_NDM (27/29, 93%).

CONCLUSIONS

Gut colonisation of neonates by AMR organisms was common and occurred rapidly in NNUs in Kenya and Nigeria. Active surveillance of colonisation will improve the understanding of AMR in these settings and guide infection control and antibiotic prescribing practice to improve clinical outcomes.

Conversations in the Gut: The Role of Quorum Sensing in Normobiosis

An imbalance in gut microbiota, termed dysbiosis, has been shown to affect host health. Several factors, including dietary changes, have been reported to cause dysbiosis with its associated pathologies that include inflammatory bowel disease, cancer, obesity, depression, and autism. We recently demonstrated the inhibitory effects of artificial sweeteners on bacterial quorum sensing (QS) and proposed that QS inhibition may be one mechanism behind such dysbiosis. QS is a complex network of cell-cell communication that is mediated by small diffusible molecules known as autoinducers (AIs). Using AIs, bacteria interact with one another and coordinate their gene expression based on their population density for the benefit of the whole community or one group over another. Bacteria that cannot synthesize their own AIs secretly "listen" to the signals produced by other bacteria, a phenomenon known as "eavesdropping". AIs impact gut microbiota equilibrium by mediating intra- and interspecies interactions as well as interkingdom communication. In this review, we discuss the role of QS in normobiosis (the normal balance of bacteria in the gut) and how interference in QS causes gut microbial imbalance. First, we present a review of QS discovery and then highlight the various QS signaling molecules used by bacteria in the gut. We also explore strategies that promote gut bacterial activity via QS activation and provide prospects for the future.

The influence of maternal factors on the neonatal microbiome and health

The human microbiome plays an essential role in human health. However, the influence of maternal factors on the neonatal microbiome remains obscure. Herein, our observations suggest that the neonatal buccal microbiome is similar to the maternal buccal microbiome, but the neonatal gastrointestinal microbiome develops a unique composition at an early stage. The low complexity of the neonatal buccal microbiome is a hallmark of maternal and neonatal health, but that of the neonatal gastrointestinal microbiome is associated with maternal inflammation-related metabolites. Microbial infections in the maternal reproductive tract universally impact the complexity of the neonatal microbiomes, and the body site is most important in modulating the composition of the neonatal microbiomes. Additionally, maternal lipids attenuated the adverse influence of several maternal factors on the neonatal microbiomes. Finally, admission of neonates to the newborn intensive care unit is associated with sub-optimal states of the maternal buccal and rectal microbiomes and maternal health.

Average Daily Gain in Lambs Weaned at 60 Days of Age Is Correlated with Rumen and Rectum Microbiota

Colonization of gastrointestinal microbiota in mammals during early life is vital to host health. The objective of this study was to investigate whether lambs with high and low ADG have a different rumen and rectum microbial community. Thus, we investigated potential relationships between rumen and rectum microbiota and average daily gain (ADG) in weaned lambs. Sixteen lambs with similar body weights (7.63 ± 1.18 kg) were selected at 30 days of age. At 60 days of age, lambs were weaned, and ADG was calculated from 60 to 90 days. Then, two groups were generated: higher ADG (HG, 134.17 ± 13.48 g/day) and lower ADG (LG, 47.50 ± 19.51 g/day). Microbiota was evaluated at 30, 60, and 90 days of age. The final live weight and ADG at 90 days of age was higher (p < 0.05) in the HG group compared to the LG group. The maturity of bacterial and fungal communities was increased (p < 0.05) in the HG group for the 30 days vs. 90 days comparison and 60 days vs. 90 days comparison. Linear discriminant analysis effect size (LEfSe) analysis revealed a total of 18 bacterial biomarkers that are ADG-specific in the rumen and 35 bacterial biomarkers in the rectum. Meanwhile, 15 fungal biomarkers were found in the rumen and 8 biomarkers were found in the rectum. Our findings indicated that ADG is related to the rumen and rectum microbiota in lambs.

Human Gut Microbiota Plasticity throughout the Life Course

The role of the gut microbiota in human health and disease has garnered heightened attention over the past decade. A thorough understanding of microbial variation over the life course and possible ways to influence and optimize the microbial pattern is essential to capitalize on the microbiota's potential to influence human health. Here, we review our current understanding of the concept of plasticity of the human gut microbiota throughout the life course. Characterization of the plasticity of the microbiota has emerged through recent research and suggests that the plasticity in the microbiota signature is largest at birth when the microbial colonization of the gut is initiated and mode of birth imprints its mark, then decreases postnatally continuously and becomes less malleable and largely stabilized with advancing age. This continuing loss of plasticity has important implication for the impact of the exposome on the microbiota and health throughout the life course and the identification of susceptible 'windows of opportunity' and methods for interventions.

Current and future methods of probiotic therapy for necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a complex intestinal disease that primarily affects premature neonates. Given its significant mortality and morbidity, there is an urgent need to develop improved prophylactic measures against the disease. One potential preventative strategy for NEC is the use of probiotics. Although there has been significant interest for decades in probiotics in neonatal care, no clear guidelines exist regarding which probiotic to use or for which patients, and no FDA-approved products exist on the market for NEC. In addition, there is lack of agreement regarding the benefits of probiotics in neonates, as well as some concerns about the safety and efficacy of available products. We discuss currently available probiotics as well as next-generation probiotics and novel delivery strategies which may offer an avenue to capitalize on the benefits of probiotics, while minimizing the risks. Thus, probiotics may still prove to be an effective prevention strategy for NEC, although further product development and research is needed to support use in the preterm population.

An insight into the commercial piglet's microbial gut colonization: from birth towards weaning

BACKGROUND

The establishment of the gut microbiota can be influenced by several perinatal factors, including, most importantly, the maternal microbiota. Moreover, early-life environmental variation affects gut microbial colonization and the intestinal health of offspring throughout life. The present study aimed to explore the development of piglet gut microbiota from birth to weaning in the commercial practice and also to assess how different farm environments could condition this process. Although it is possible to find in the literature other studies with similar objectives this work probably represents one of the few studies that make a systematic evaluation of such differential factors under a real scenario. To achieve this objective, we performed two trials. In a first Trial, we selected 2 farms in which we performed an intensive sampling (5 samples /animal) to characterize the gut colonization pattern during the first days of life and to identify the time window with the greatest impact. Both farms differed in their health status and the use of antimicrobials in the piglets. In a second Trial, we selected 4 additional farms with variable rearing conditions and a distinctive use of antimicrobials in the sows with a simplified sampling pattern (2 samples/animal). Faecal samples were obtained with swabs and DNA was extracted by using the PSP® Spin Stool DNA Kit and sequencing of the 16S rRNA gene (V3-V4 region) performed by Illumina MiSeq Platform.

RESULTS

The present study contributes to a better understanding of microbiome development during the transition from birth to weaning in commercial conditions. Alpha diversity was strongly affected by age, with an increased richness of species through time. Beta diversity decreased after weaning, suggesting a convergent evolvement among individuals. We pinpointed the early intestinal colonizers belonging to Bacteroides, Escherichia-Shigella, Clostridium sensu stricto 1, and Fusobacterium genera. During lactation(d7-d21 of life), the higher relative abundances of Bacteroides and Lactobacillus genera were correlated with a milk-oriented microbiome. As the piglets aged and after weaning (d36 of life), increasing abundances of genera such as Prevotella, Butyricimonas, Christensenellaceae R-7 group, Dorea, Phascolarctobacterium, Rikenellaceae RC9 gut group, Subdoligranulum, and Ruminococcaceae UCG-002 were observed. These changes indicate the adaptation of the piglets to a cereal-based diet rich in oligosaccharides and starch. Our results also show that the farm can have a significant impact in such a process, evidencing the influence of different environments and rearing systems on the gut microbiota development of the young piglet. Differences between farms were more noticeable after weaning than during lactation with changes in alpha and beta biodiversity and specific taxa. The analysis of such differences suggests that piglets receiving intramuscular amoxicillin (days 2-5 of life) and being offered an acidifying rehydrating solution (Alpha farm in Trial 1) have a greater alpha diversity and more abundant Lactobacillus population. Moreover, the only farm that did not offer any rehydrating solution (Foxtrot farm in Trial 2) showed a lower alpha diversity (day 2 of life) and increased abundance of Enterobacteriaceae (both at 2 and 21 days). The use of in-feed antibiotics in the sows was also associated with structural changes in the piglets' gut ecosystem although without changes in richness or diversity. Significant shifts could be registered in different microbial groups, particularly lower abundances of Fusobacterium in those piglets from medicated sows.

CONCLUSIONS

In conclusion, during the first weeks of life, the pig microbiota showed a relevant succession of microbial groups towards a more homogeneous and stable ecosystem better adapted to the solid dry feed. In this relevant early-age process, the rearing conditions, the farm environment, and particularly the antimicrobial use in piglets and mothers determine changes that could have a relevant impact on gut microbiota maturation. More research is needed to elucidate the relative impact of these farm-induced early life-long changes in the growing pig.

Effects of early postnatal life nutritional interventions on immune-microbiome interactions in the gastrointestinal tract and implications for brain development and function

The gastrointestinal (GI) microbiota has co-evolved with the host in an intricate relationship for mutual benefit, however, inappropriate development of this relationship can have detrimental effects. The developing GI microbiota plays a vital role during the first 1,000 days of postnatal life, during which occurs parallel development and maturation of the GI tract, immune system, and brain. Several factors such as mode of delivery, gestational age at birth, exposure to antibiotics, host genetics, and nutrition affect the establishment and resultant composition of the GI microbiota, and therefore play a role in shaping host development. Nutrition during the first 1,000 days is considered to have the most potential in shaping microbiota structure and function, influencing its interactions with the immune system in the GI tract and consequent impact on brain development. The importance of the microbiota-GI-brain (MGB) axis is also increasingly recognized for its importance in these developmental changes. This narrative review focuses on the importance of the GI microbiota and the impact of nutrition on MGB axis during the immune system and brain developmental period in early postnatal life of infants.

A systematic review of breast milk microbiota composition and the evidence for transfer to and colonisation of the infant gut

The intestinal microbiota plays a major role in infant health and development. However, the role of the breastmilk microbiota in infant gut colonisation remains unclear. A systematic review was performed to evaluate the composition of the breastmilk microbiota and evidence for transfer to/colonisation of the infant gut. Searches were performed using PUBMED, OVID, LILACS and PROQUEST from inception until 18th March 2020 with a PUBMED update to December 2021. 88 full texts were evaluated before final critique based on study power, sample contamination avoidance, storage, purification process, DNA extraction/analysis, and consideration of maternal health and other potential confounders. Risk of skin contamination was reduced mainly by breast cleaning and rejecting the first milk drops. Sample storage, DNA extraction and bioinformatics varied. Several studies stored samples under conditions that may selectively impact bacterial DNA preservation, others used preculture reducing reliability. Only 15 studies, with acceptable sample size, handling, extraction, and bacterial analysis, considered transfer of bacteria to the infant. Three reported bacterial transfer from infant to breastmilk. Despite consistent evidence for the breastmilk microbiota, and recent studies using improved methods to investigate factors affecting its composition, few studies adequately considered transfer to the infant gut providing very little evidence for effective impact on gut colonisation.

Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium

In vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the “infant-like” gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.

Oral polio revaccination is associated with changes in gut and upper respiratory microbiomes of infants

After the eradication of polio infection, the plan is to phase-out the live-attenuated oral polio vaccine (OPV). Considering the protective non-specific effects (NSE) of OPV on unrelated pathogens, the withdrawal may impact child health negatively. Within a cluster-randomized trial, we carried out 16S rRNA deep sequencing analysis of fecal and nasopharyngeal microbial content of Bissau–Guinean infants aged 4–8 months, before and after 2 months of OPV revaccination (revaccinated infants = 47) vs. no OPV revaccination (control infants = 47). The aim was to address changes in the gut and upper respiratory bacterial microbiotas due to revaccination. Alpha-diversity for both microbiotas increased similarly over time in OPV-revaccinated infants and controls, whereas greater changes over time in the bacterial composition of gut (padjusted &lt; 0.001) and upper respiratory microbiotas (padjusted = 0.018) were observed in the former. Taxonomic analysis of gut bacterial microbiota revealed a decrease over time in the median proportion of Bifidobacterium longum for all infants (25–14.3%, p = 0.0006 in OPV-revaccinated infants and 25.3–11.6%, p = 0.01 in controls), compatible with the reported weaning. Also, it showed a restricted increase in the median proportion of Prevotella_9 genus in controls (1.4–7.1%, p = 0.02), whereas in OPV revaccinated infants an increase over time in Prevotellaceae family (7.2–17.4%, p = 0.005) together with a reduction in median proportion of potentially pathogenic/opportunistic genera such as Escherichia/Shigella (5.8–3.4%, p = 0.01) were observed. Taxonomic analysis of upper respiratory bacterial microbiota revealed an increase over time in median proportions of potentially pathogenic/opportunistic genera in controls, such as Streptococcus (2.9–11.8%, p = 0.001 and Hemophilus (11.3–20.5%, p = 0.03), not observed in OPV revaccinated infants. In conclusion, OPV revaccination was associated with a healthier microbiome composition 2 months after revaccination, based on a more abundant and diversified bacterial community of Prevotellaceae and fewer pathogenic/opportunistic organisms. Further information on species-level differentiation and functional analysis of microbiome content are warranted to elucidate the impact of OPV-associated changes in bacterial microbiota on child health.

The role of the gut microbiota in health and cardiovascular diseases

The gut microbiota is critical to human health, such as digesting nutrients, forming the intestinal epithelial barrier, regulating immune function, producing vitamins and hormones, and producing metabolites to interact with the host. Meanwhile, increasing evidence indicates that the gut microbiota has a strong correlation with the occurrence, progression and treatment of cardiovascular diseases (CVDs). In patients with CVDs and corresponding risk factors, the composition and ratio of gut microbiota have significant differences compared with their healthy counterparts. Therefore, gut microbiota dysbiosis, gut microbiota-generated metabolites, and the related signaling pathway may serve as explanations for some of the mechanisms about the occurrence and development of CVDs. Several studies have also demonstrated that many traditional and latest therapeutic treatments of CVDs are associated with the gut microbiota and its generated metabolites and related signaling pathways. Given that information, we summarized the latest advances in the current research regarding the effect of gut microbiota on health, the main cardiovascular risk factors, and CVDs, highlighted the roles and mechanisms of several metabolites, and introduced corresponding promising treatments for CVDs regarding the gut microbiota. Therefore, this review mainly focuses on exploring the role of gut microbiota related metabolites and their therapeutic potential in CVDs, which may eventually provide better solutions in the development of therapeutic treatment as well as the prevention of CVDs.

Maternal weight status and the composition of the human milk microbiome: A scoping review

The human milk microbiome is thought to partly contribute to the assembly of the infant gut microbiome, a microbial community with important implications for infant health and development. While obesity has well-established links with the adult gut microbiome, less is known about how it affects the human milk microbiome. In this scoping review, we synthesize the current literature on the microbial composition of human milk by maternal weight status, defined broadly as BMI (prepregnancy and postpartum) and gestational weight gain (GWG). This study followed the a priori protocol published in Prospero (registration #: CRD42020165633). We searched the following databases for studies reporting maternal weight status and a characterization of milk microbiota through culture-dependent and culture-independent methods: MEDLINE, Embase, Web of Science, CINAHL, and Scopus. After screening 6,365 studies, we found 20 longitudinal and cross-sectional studies investigating associations between maternal weight status and the composition of the milk microbiome. While some studies reported no associations, many others reported that women with a pre-pregnancy or postpartum BMI characterized as overweight or obese, or with excessive GWG, had higher abundances of the genus Staphylococcus, lower Bifidobacterium abundance, and lower alpha diversity (within-sample diversity). This review suggests that maternal weight status is minorly associated with the composition of the milk microbiome in various ways. We offer potential explanations for these findings, as well as suggestions for future research.

The Resemblance between Bacterial Gut Colonization in Pigs and Humans

Thorough understanding of the initial colonization process of human intestines is important to optimize the prevention of microbiota-associated diseases, and also to further improve the current microbial therapies. In recent years, therefore, colonization of the human gut has gained renewed interest. However, due to a lack of standardization of life events that might influence this early colonization process in humans, many generally accepted insights are based on deduction and assumption. In our review, we compare knowledge on colonization in humans with research in piglets, because the intestinal tract of pigs is remarkably similar to that of humans and the early-life events are more standardized. We assess potential similarities and challenge some concepts that have been widely accepted in human microbiota research. Bacterial colonization of the human gut is characterized by successive waves in a progressive process, to a complex gut microbiota community. After re-analyzing available data from piglets, we found that the bacterial colonization process is very similar in terms of the wave sequence and functionality of each wave. Moreover, based on the piglet data, we found that, in addition to external factors such as suckling and nutrition, the bacterial community itself appears to have a major influence on the colonization success of additional bacteria in the intestine. Thus, the colonization process in piglets might rely, at least in part, on niche dependency, an ecological principle to be considered in the intestinal colonization process in humans.

Neonatal Streptococcus pneumoniae infection induces long-lasting dysbiosis of the gut microbiota in a mouse model

Early life is a “critical window” for gut microbiota development, antibiotic use during this period exerts a profound effect on gut microbial dysbiosis and asthma. In clinical practice, antibiotics are usually used in patients with bacterial infections, we previously showed that neonatal S. pneumoniae pneumonia promoted adult-onset asthma in mice model, while it remains unclear whether neonatal S. pneumoniae infection have long-term effects on gut microbiota. Neonatal BALB/c mice were inoculated with 5*10⁶ CFU D39 to establish non-lethal S. pneumoniae pneumonia model. At 2, 3, 8 weeks of age, feces in the cecum were prepared for 16S rRNA sequencing, lungs were collected for histopathologic and lung function analysis. S. pneumoniae-infected neonatal mice exhibited histopathologic lesions in their lungs and increased airway hyperresponsiveness, obvious alterations in alpha and beta diversities in the entire gut microbiota, and changes of the community structure during the breastfeeding period, infancy, and adulthood. Furthermore, gut microbial composition was modified after neonatal S. pneumoniae infection, with a decreased relative abundance of Lactobacillus in the breastfeeding period and infancy; in adulthood, the relative abundance of Allobaculum diminished while that of Proteobacteria was augmented. Neonatal S. pneumoniae infection induced a long-term alteration in microbial community composition.

The Complex Link and Disease Between the Gut Microbiome and the Immune System in Infants

The human gut microbiome is important for human health. The development of stable microbial communities in the gastrointestinal tract is closely related to the early growth and development of host immunity. After the birth of a baby, immune cells and the gut microbiome mature in parallel to adapt to the complex gut environment. The gut microbiome is closely linked to the immune system and influences each other. This interaction is associated with various diseases in infants and young children, such as asthma, food allergies, necrotizing colitis, obesity, and inflammatory bowel disease. Thus, the composition of the infant gut microbiome can predict the risk of disease development and progression. At the same time, the composition of the infant gut microbiome can be regulated in many ways and can be used to prevent and treat disease in infants by modulating the composition of the infant gut microbiome. The most important impacts on infant gut microbiota are maternal, including food delivery and feeding. The differences in the gut microbiota of infants reflect the maternal gut microbiota, which in turn reflects the gut microbiota of a given population, which is clinically significant.

Selective Maternal Seeding and Rearing Environment From Birth to Weaning Shape the Developing Piglet Gut Microbiome

The acquisition and development of the mammalian microbiome early in life are critical to establish a healthy host-microbiome symbiosis. Despite recent advances in understanding microbial sources in infants, the relative contribution of various microbial sources to the colonization of the gut microbiota in pigs remains unclear. Here, we longitudinally sampled the microbiota of 20 sow-piglet pairs (three piglets per sow) reared under identical conditions from multiple body sites and the surrounding weaning environment from birth to 28 days postpartum (1,119 samples in total). Source-tracking analysis revealed that the contribution of various microbial sources to the piglet gut microbiome gradually changed over time. The neonatal microbiota was initially sparsely populated, and the predominant contribution was from the maternal vaginal microbiota that increased gradually from 69.0% at day 0 to 89.3% at day 3 and dropped to 0.28% at day 28. As the piglets aged, the major microbial community patterns were most strongly associated with the sow feces and slatted floor, with contributions increasing from 0.52 and 9.6% at day 0 to 62.1 and 33.8% at day 28, respectively. The intestinal microbial diversity, composition, and function significantly changed as the piglets aged, and 30 age-discriminatory bacterial taxa were identified with distinctive time-dependent shifts in their relative abundance, which likely reflected the effect of the maternal and environmental microbial sources on the selection and adaptation of the piglet gut microbiota. Overall, these data demonstrate that the vaginal microbiota is the primary source of the gut microbiota in piglets within 3 days after birth and are gradually replaced by the sow fecal and slatted floor microbiota over time. These findings may offer novel strategies to promote the establishment of exogenous symbiotic microbes to improve piglet gut health.

Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

Microbiota colonization is a dynamic process that impacts the health status during an individual's lifetime. The composition of the gut microbiota of newborns is conditioned by multiple factors, including the delivery mode (DM). Nonetheless, the DM's influence remains uncertain and is still the subject of debate. In this context, the medical indication and the emergency of a cesarean delivery might have led to confounding conclusions regarding the composition and diversity of the neonatal microbiome. Herein, we used high-resolution shotgun sequencing to decipher the composition and dynamics of the gut microbiota composition of Tunisian newborns. Stool samples were collected from 5 elective cesarean section (ECS) and 5 vaginally delivered (VD) newborns at the following time points: Day 0, Day 15, and Day 30. The ECS and VD newborns showed the same level of bacterial richness and diversity. In addition, our data pointed to a shift in microbiota community composition during the first 2 weeks, regardless of the DM. Both ECS and VD showed a profile dominated by Proteobacteria, Actinobacteria, and Firmicutes. However, ECS showed an underrepresentation of Bacteroides and an enrichment of opportunistic pathogenic species of the ESKAPE group, starting from the second week. Besides revealing the intestinal microbiota of Tunisian newborns, this study provides novel insights into the microbiota perturbations caused by ECS.

Early life host-microbe interactions in skin

Our skin is the interface through which we mediate lifelong interactions with our surrounding environment. Initial development of the skin's epidermis, adnexal structures, and barrier function is necessary for normal cutaneous microbial colonization, immune development, and prevention of disease. Early life microbial exposures can have unique and long-lasting impacts on skin health. The identity of neonatal skin microbes and the context in which they are first encountered, i.e., through a compromised skin barrier or in conjunction with cutaneous inflammation, can have additional short- and long-term health consequences. Here, we discuss key attributes of infant skin and endogenous and exogenous factors that shape its relationship to the early life cutaneous microbiome, with a focus on their clinical implications.

The human milk microbiome aligns with lactation stage and not birth mode

We analysed the human milk microbiome in a cohort of 80 lactating women and followed the dynamics in taxa over the course of lactation from birth to 6 months. Two hundred and thirty one milk samples were collected from full-term lactating women at 1, 4, 8 and 24 weeks following birth and analysed for microbiota composition using 16S rRNA sequencing. A significant decrease in milk microbiota diversity was observed throughout the first 6 months of lactation, with the greatest difference seen between week 8 and week 24. Nine genera predominated in milk over lactation from week 1 to week 24, comprising of Staphylococcus, Streptococcus, Pseudomonas, Acinetobacter, Bifidobacterium, Mesorhizobium, Brevundimonas, Flavobacterium, and Rhodococcus; however, fluctuations in these core genera were apparent over time. There was a significant effect of stage of lactation on the microbiome, while no effect of birth mode, infant sex and maternal BMI was observed throughout lactation. Streptococcus had the highest mean relative abundance at week 1 and 24 (17.3% and 24% respectively), whereas Pseudomonas predominated at week 4 (22%) and week 8 (19%). Bifidobacterium and Lactobacillus had the highest mean relative abundance at week 4 (5% and 1.4% respectively), and occurred at a relative abundance of ≤ 1% at all other time points. A decrease in milk microbiota diversity throughout lactation was also observed. This study concluded that lactation stage was the primary driving factor in milk microbiota compositional changes over lactation from birth to 6 months, while mode of delivery was not a factor driving compositional changes throughout human lactation.

Identifying biomarkers of the gut bacteria, bacteriophages and serum metabolites associated with three weaning periods in piglets

Background

The establishment of the piglet gut microbiome has a prolonged influence on host health, as it sets the stage for establishment of the adult swine microbiome. Substantial changes in host metabolism and immunity around the time of weaning may be accompanied by alterations in the gut microbiome. In this study, we systematically evaluated differences in the gut microbiome and host metabolites among three weaning periods using shotgun metagenomic sequencing and untargeted metabolomic profiling in piglets.

Results

We identified that P. copri was the most significantly different species among three weaning periods, and was the key bacterial species for mitigating piglet adaptation during the weaning transition, while Bacillus_phage_BCD7, the only differential bacteriophages, was significantly and positively correlated with P. copri enriched in day 28 group. Additionally, P. copri and Bacillus_phage_BCD7 was significantly correlated with the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, the altered metabolites we observed were enriched in pathways matched to the functional capacity of the gut microbiome e.g., aminoacyl-tRNA biosynthesis.

Conclusion

The results from this study indicate that the bacteria-phage interactions and host-microbial interactions during the weaning transition impact host metabolism, leading to beneficial host changes among three weaning periods.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03203-w.

The Macronutrient Composition of Infant Formula Produces Differences in Gut Microbiota Maturation That Associate with Weight Gain Velocity and Weight Status

This proof-of-principle study analyzed fecal samples from 30 infants who participated in a randomized controlled trial on the effects of the macronutrient composition of infant formula on growth and energy balance. In that study, infants randomized to be fed cow milk formula (CMF) had faster weight-gain velocity during the first 4 months and higher weight-for-length Z scores up to 11.5 months than those randomized to an isocaloric extensive protein hydrolysate formula (EHF). Here we examined associations among infant formula composition, gut microbial composition and maturation, and children’s weight status. Fecal samples collected before and monthly up to 4.5 months after randomization were analyzed by shotgun metagenomic sequencing and targeted metabolomics. The EHF group had faster maturation of gut microbiota than the CMF group, and increased alpha diversity driven by Clostridia taxa. Abundance of Ruminococcus gnavus distinguished the two groups after exclusive feeding of the assigned formula for 3 months. Abundance of Clostridia at 3–4 months negatively correlated with prior weight-gain velocity and body weight phenotypes when they became toddlers. Macronutrient differences between the formulas likely led to the observed divergence in gut microbiota composition that was associated with differences in transient rapid weight gain, a well-established predictor of childhood obesity and other comorbidities.

Oral administration of Lactobacillus delbrueckii enhances intestinal immunity through inducing dendritic cell activation in suckling piglets

Lactobacillus delbrueckii (LAB) has been demonstrated to exert versatile beneficial effects on modulating intestinal immunity, increasing gut microbial diversity, promoting growth performance, and even preventing disease onset in pigs. However, the underlying mechanism of LAB-mediated gut immunity regulation in piglets remains unclear. In this study, we found that supplementation of LAB significantly increases serum TNF-α, ileum IL-4, and IL-10 levels compared with the control group. Meanwhile, oral supplementation of LAB-modified gut microbial communities was evidenced by the increased abundance of the Lactobacillus genus in the colon. Mechanistically, LAB induced dendritic cell (DC) maturation and activation, which may be relevant to the activation of NF-κB and MAPK signaling pathways. Moreover, we found that oral administration of LAB during the suckling period shows long-lasting immunomodulatory impacts on intestinal immunity after weaning. Collectively, this study uncovers the mechanism of LAB in regulating the intestinal immunity of piglets, suggesting that LAB can be developed as an immunoenhancing biological agent during the suckling period.