Establishment of the bacterial fecal community during the first month of life in Brazilian newborns

Social vulnerability among Brazilian children in early childhood: a scoping review

OBJECTIVE

To identify, map, and describe studies involving Brazilian children in early childhood in situations of social vulnerability.

SOURCE OF DATA

A scoping review including full articles published in Portuguese and English up to March 2023, with no temporal restrictions. Searches were conducted in the MEDLINE/PubMed, Scielo, EMBASE, Cochrane, Scopus, CINAHL, Web of Science, PEDro, and LILACS databases. Journal metrics, sample characteristics, study area, characterization of the situation of social vulnerability, and study outcomes were extracted.

SUMMARY OF THE FINDINGS

Seventy-six articles involving a total of 107.740 children in early childhood were included in this study. These studies presented relevant findings, including the temporal publication trend, the variability of social vulnerability indicators, the scarcity of intervention studies, and the fact that 100% of eligible studies were from the health area. Negative outcomes were associated with the condition of social vulnerability in almost the entire sample, reinforcing the need for government policies capable of protecting early childhood from the effects of social vulnerability.

CONCLUSION

This scoping review mapped important findings involving Brazilian children in social vulnerability. It also identified literature gaps such as the need for intervention and multisectoral studies among health, education, and social protection.

Longitudinal 16S rRNA gut microbiota data of infant triplets show partial susceptibility to host genetics

The question of whether host genetics plays a role in the development of the infant gut microbiota does not, as yet, have a clear answer. In order to throw additional light on this question, we have analyzed 16S rRNA amplicon sequences from 99 valid fecal samples of five sets of dichorionic triplet babies born by C-section from 1 to 36 months of age. Beta diversity analysis showed that monozygotic twins were more similar to each other than their dizygotic siblings. Monozygotic twins also tended to share more amplicon sequence variants between them. Heritability analysis showed that the genera Bacteroides and Veillonella are particularly susceptible to host genetics. We conclude that infant gut microbiota development is influenced by host genetics, but this effect is subtle and may affect only certain bacterial taxa during a limited time period early in life.

Evolution of Intestinal Microbiota of Asphyxiated Neonates Within 1 Week and Its Relationship With Neural Development at 6 Months

Introduction: Asphyxia is an emergent condition in neonates that may influence the function of the nervous system. Research has shown that intestinal microbiota is very important for neurodevelopment. Studies regarding the association between gut microbiota and neurodevelopment outcome in asphyxiated newborns remain scarce. Objective: To study the microbial characteristics of asphyxiated neonates within 1 week of life and to investigate their relationship with neural development at 6 months. Methods: The feces produced on days 1, 3, and 5, and the clinical data of full-term neonates with asphyxia and without asphyxia, delivered from March 2019 to October 2020 at Peking University First Hospital, were collected. We used 16S ribosomal deoxyribonucleic acid amplicon sequencing to detect the intestinal microbiota of asphyxiated neonates and neonates in the control group. We followed up asphyxiated neonates for 6 months and used the Ages and Stages Questionnaires-3 (ASQ-3) to evaluate their development. Results: A total of 45 neonates were enrolled in the study group and 32 were enrolled in the control group. On day 1, the diversity and richness of the microflora of the study group were more than those of the control group. Non-metric multidimensional scaling analysis showed significant differences in the microbiota of the two groups on days 1, 3, and 5. At the phylum level, the main microflora of the two groups were not different. At the genus level, the study group had increased relative abundance of Clostridium_sensu_stricto_1, Lachnoclostridium, Fusicatenibacter, etc. on day 1. On day 3, the relative abundance of Clostridium_sensu_stricto_1, Fusicatenibacter, etc. was still greater than that of the control group, and the relative abundance of Staphylococcus was less than that of the control group. On day 5, the relative abundance of Clostridium_sensu_stricto_1 and Lachnoclostridium was still higher than that of the control group, and the relative abundance of Dubosiella in the study group was significantly increased. At the species level, on day 3, the relative abundance of Staphylococcus caprae in the study group was less than that in the control group. Linear discriminant analysis effect size showed that the microbiota of the study group mainly consisted of Lachnospiraceae and Clostridia on day 1 and Clostridia on day 3. In the control group, Staphylococcus was the dominant bacterium on day 3. Neonates in the study group were followed up for 6 months, and the communication score of ASQ-3 was negatively correlated with the relative abundance of Lachnospiraceae and Clostridia on day 1. Conclusion: The diversity and richness of the microbiota of asphyxiated neonates on the first day of life were significantly increased and mainly consisted of pathogenic flora. Lachnospiraceae and Clostridia found in neonates with asphyxia on day 1 of life may be related to neural development at 6 months.

Gut microbiota comparison of vaginally and cesarean born infants exclusively breastfed by mothers secreting α1-2 fucosylated oligosaccharides in breast milk

BACKGROUND

Exclusive breastfeeding promotes beneficial modifications on the microbiota of cesarean born infants, but little is known about the role of specific breast milk components in this modulation. Women with an active FUT2 gene (called secretors) secrete α1-2 fucosylated human milk oligosaccharides (HMOs), which promote Bifidobacterium in the infant's gut and may modulate the microbiota of cesarean born infants.

OBJECTIVE

To compare the microbiota composition of cesarean and vaginally born infants breastfed by secretor mothers.

METHODS

Maternal secretor status was determined by the occurrence of 4 different α1-2 fucosylated HMOs in breast milk by LC-MS. The fecal microbiota composition from cesarean and vaginally born infants was analyzed by 16S rRNA gene sequencing and qPCR, stratified by the maternal secretor status, and compared.

RESULTS

Alpha and beta diversity were not significantly different in cesarean born, secretor-fed infants (CSe+) compared to vaginally born, secretor-fed infants (VSe+). There were no significant differences in the fecal relative abundance of Bifidobacterium between CSe+ and VSe+ infants, but the prevalence of the species B. longum was lower in CSe+. The fecal relative abundance of Bacteroides was also lower, while Akkermansia and Kluyvera were higher in CSe+ infants.

CONCLUSION

Cesarean and vaginally born infants fed with breast milk containing the α1-2 fucosylated HMOs fraction present similar amounts of Bifidobacterium in the feces, but differences are observed in other members of the microbiota.

Gut Microbiota of Young Children Living in Four Brazilian Cities

Recent studies have demonstrated that gut microbiota development is influenced by human biogeographic factors such as race, ethnicity, diet, lifestyle or culture-specific variations, and other environmental influences. However, biogeographic variation in gut microbiota assembly remains largely unexplored in Latin America. In this paper, we compared food recall information and microbiota composition of toddlers living in geographically separated urban populations within four states of Brazil. 16S RNA gene sequencing revealed that alpha diversity was similar between the four different populations. Gut microbiota compositions were dominated by members of the phyla Firmicutes and Bacteroidetes, resembling a more adult-like microbiota as compared with those of Western European toddlers of similar age. These findings suggest that inter-individual and nutrition-induced differences were apparent in the fecal microbiota. We conclude that urban dietary pattern plays a larger role in influencing the gut microbiota composition than do biogeographic factors.

Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants

Colonization of the gastrointestinal tract with microorganisms during infancy represents a critical control point for shaping life-long immune-mediated disease susceptibility. Abnormal colonization or an imbalance of microbes, termed dysbiosis, is implicated in several diseases. Consequently, recent research has aimed at understanding ways to manipulate a dysbiotic microbiome during infancy to resemble a normal, healthy microbiome. However, one of the fundamental issues in microbiome research is characterizing what a "normal" infant microbiome is based on geography, ethnicity and cultural variations. This review provides a comprehensive account of what is currently known about the infant microbiome from a global context. In general, this review shows that the influence of cultural variations in feeding practices, delivery modes and hygiene are the biggest contributors to microbial variability. Despite geography or race, all humans have similar microbial succession during infancy.

Maternal antibiotic prophylaxis affects Bifidobacterium spp. counts in the human milk, during the first week after delivery

Human milk is an important source of microorganisms for infant gut colonisation. Although the maternal antibiotic prophylaxis is an important strategy to prevent maternal/neonatal sepsis, it has to be investigated how it may affect the human milk microbiota, especially the genus Bifidobacterium, which has been associated to health benefits. Here, we investigated the impact of the maternal antibiotic prophylaxis on the human milk Bifidobacterium spp. and total bacteria counts, in the first week (short-term) and first month (medium-term) after delivery. Human milk samples were collected from 55 healthy lactating women recruited from the University Hospital of the University of São Paulo at days 7±3 and 30±4 after vaginal delivery. Twenty one volunteers had received maternal antibiotic prophylaxis (MAP group) and 34 had not received MAP (no-MAP group) during or after labour. Total DNA was isolated from milk samples, and the bacterial counts were estimated by quantitative PCR (qPCR). We found lower levels of Bifidobacterium in the MAP group in the first week after delivery (median = 2.1 vs 2.4 log of equivalent cells/ml of human milk, for MAP and no-MAP groups, respectively; P=0.01), although there were no statistical differences in total bacteria count. However, no differences were found in Bifidobacterium counts between the groups at day 30±4 (median = 2.5 vs 2.2 log of equivalent cells/ml of human milk, for MAP and no-MAP groups, respectively; P=0.50). Our results suggest that MAP has a significant impact on Bifidobacterium counts in human milk, reducing this population in the first week after delivery. However, throughout the first month after delivery, the Bifidobacterium counts tend to recover, reaching similar counts to those found in no-MAP group at day 30±4 after delivery.

Breastfeeding increases microbial community resilience

OBJECTIVE

Since the present group had already described the composition of the intestinal microbiota of Brazilian infants under low social economic level, the aim of the present study was to analyze the microbial community structure changes in this group of infants during their early life due to external factors.

METHODS

Fecal samples were collected from 11 infants monthly during the first year of life. The infants were followed regarding clinical and diet information and characterized according to breastfeeding practices. DNA was extracted from fecal samples of each child and subjected to Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis.

RESULTS

The results revealed a pattern of similarity between the time points for those who were on exclusive breastfeeding or predominant breastfeeding. Although there were changes in intensity and fluctuation of some bands, the Denaturing Gradient Gel Electrophoresis patterns in the one-year microbial analysis were stable for breastfeeding children. There was uninterrupted ecological succession despite the influence of external factors, such as complementary feeding and antibiotic administration, suggesting microbiota resilience. This was not observed for those children who had mixed feeding and introduction of solid food before the 5^th month of life.

CONCLUSION

These results suggested an intestinal microbiota pattern resilient to external forces, due to the probiotic and prebiotic effects of exclusive breastfeeding, reinforcing the importance of exclusive breastfeeding until the 6^th month of life.

The human gut microbiome of Latin America populations: a landscape to be discovered

PURPOSE OF REVIEW

The gut microbiome is critical for human health, and its alteration is associated with intestinal, autoimmune and metabolic diseases. Numerous studies have focused on prevention or treatment of dysbiotic microbiome to reduce the risk or effect of these diseases. A key issue is to define the microbiome associated with the state of good health. The purpose of this review is to describe factors influencing the gut microbiome with special emphasis on contributions from Latin America. In addition, we will highlight opportunities for future studies on gut microbiome in Latin America.

RECENT FINDINGS

A relevant factor influencing gut microbiome composition is geographical location associated with specific genetic, dietary and lifestyle factors. Geographical specificities suggest that a universal 'healthy microbiome' is unlikely.

SUMMARY

Several research programs, mostly from Europe and North America, are extensively sequencing gut microbiome of healthy people, whereas data from Latin America remain scarce yet slowly increasing. Few studies have shown difference in the composition of gut microbiome between their local populations with that of other industrialized countries (North American populations). Latin America is composed of countries with a myriad of lifestyles, traditions, genetic backgrounds and socioeconomic conditions, which may determine differences in gut microbiome of individuals from different countries. This represents an opportunity to better understand the relationship between these factors and gut microbiome.

Anaerobic bacteria in the intestinal microbiota of Brazilian children

OBJECTIVE:

Changes in the neonatal gut environment allow for the colonization of the mucin layer and lumen by anaerobic bacteria. The aim of the present study was to evaluate Bifidobacterium, Lactobacillus and Lactococcus colonization through the first year of life in a group of 12 Brazilian infants and to correlate these data with the levels of Escherichia coli. The presence of anaerobic members of the adult intestinal microbiota, including Eubacterium limosum and Faecalibacterium prausnitzii, was also evaluated.

METHODS:

Fecal samples were collected during the first year of life, and 16S rRNA from anaerobic and facultative bacteria was detected by real-time PCR.

RESULTS:

Bifidobacterium was present at the highest levels at all of the studied time points, followed by E. coli and Lactobacillus. E. limosum was rarely detected, and F. prausnitzii was detected only in the samples from the latest time points.

CONCLUSION:

These results are consistent with reports throughout the world on the community structure of the intestinal microbiota in infants fed a milk diet. Our findings also provide evidence for the influence of the environment on intestinal colonization due to the high abundance of E. coli. The presence of important anaerobic genera was observed in Brazilian infants living at a low socioeconomic level, a result that has already been well established for infants living in developed countries.

Intestinal Bacterial Colonization in the First 2 Weeks of Life of Nigerian Neonates Using Standard Culture Methods

OBJECTIVE

The pattern and timing of development of intestinal microflora in Nigerian infants have been scarcely researched. This study was carried out to investigate the bacteria flora in the rectum of healthy neonates in Ibadan, Nigeria.

PATIENTS AND METHODS

In this hospital-based longitudinal study, rectal swabs of 70 neonates were taken within 6-12 h of birth (day 1) and subsequently on days 3, 9, and 14. Information collected included maternal sociodemographic characteristics, antibiotic use for the neonates, and type of feeding during the first 14 days of life. Identification and speciation of gram-negative isolates were done using the Analytical Profile Index 20E® and 20NE® as appropriate. Gram-positive bacteria were identified biochemically using the catalase and coagulase tests. Data were analyzed using descriptive statistics and Chi-square at p = 0.05.

RESULTS

Majority (92.9%) of the neonates were delivered vaginally with a median gestational age of 38 weeks (range = 34-42). On the first day of life, Escherichia coli was isolated more frequently from the rectal swabs of preterm (50.0%) than term (23.1%) neonates (p = 0.031). On day 3 of life, coagulase-negative staphylococcus was the most frequently isolated bacteria from the rectal swabs of nonasphyxiated (64.4%) compared with asphyxiated (27.3%) neonates' rectal swabs (p = 0.042). Staphylococcus aureus was the most frequently isolated bacteria from the rectal swabs of nonexclusively breastfed (66.7%) than exclusively breastfed (21.3%) neonates on day 14 (p = 0.004).

CONCLUSION

Staphylococcus aureus and Escherichia coli were the predominant isolates from the rectum of Nigerian neonates, and these isolates were influenced by breastfeeding and mild-moderate asphyxia. In all, bacterial diversity in the rectum increased as the neonates got older.

Development of the infant intestinal microbiome: A bird's eye view of a complex process

Infants undergo profound shifts in colonizing intestinal microorganisms during their first year, especially during and after birth and during weaning. Microbiota are passed to infants through the placenta, during the vaginal birth process, and from early diet and other environmental exposures. These microbiota play an active role in the development of healthy infant metabolic and immunologic systems; profound shifts in microbiotal populations can be persistent, are associated with immediate alterations in gene expression, metabolic, immunologic, and neurologic function, and with downstream metabolic and immunologic consequences such as obesity, allergies, asthma, autoimmune diseases, and potentially neurologic conditions. Many modern exposures, including Cesarean section, formula feeding, and antibiotics, have been associated with microbiome shifts, and also with downstream diseases; while many published studies considered exposures individually, a more comprehensive understanding of their interaction and impact will consider the entirety of the infant's environment. It is not possible, nor desirable, to return to a world without toilets, sewers, tap water, delivery room antisepsis, Cesarean sections, antibiotics, immunizations, and refrigerators; our other alternative is to better understand these complex changes in infant developmental and molecular physiology. Protecting and repairing the developmental processes of the healthy infant microbiome is the modern medical frontier.

The Early Intestinal Microbiota of Healthy Korean Newborns

Background:

The microflora hypothesis may be the underlying explanation for the growth of inflammatory disease. In addition to many known affecting factors, knowing the gut microbiota of healthy newborns can help to understand the gut immunity and modulate it.

Objectives:

This study examined the microbiota of healthy newborns from urban regions.

Patients and Methods:

We enrolled 128 full-term newborns, born at Seoul St. Mary and St. Paul hospital from January 2009 to February 2010. All 143 samples of feces were cultivated in six culture plates to determine the amounts of total bacteria, anaerobes, gram-positive bacteria, coliforms, lactobacilli, and bifidobacteria. The samples were evaluated with a bivariate correlation between coliforms and lactobacilli. Terminal restriction fragment length polymorphism (T-RFLP) analysis with HhaI and MspI and a clustering analysis were performed for determination of diversity.

Results:

Bacteria were cultured in 61.5% of feces in the following order: anaerobes, gram-positive bacteria, lactobacilli, coliform, and bifidobacteria. The growth of total bacteria and lactobacilli increased in feces defecated after 24 hours of birth (P < 0.001, P = 0.008) and anaerobes decreased (P = 0.003). A negative correlation between the growth of lactobacilli and coliforms was found (r = -463, P < 0.001).

Conclusions:

This study confirms that bacterial colonization of healthy newborns born in cities is non-sterile, but has early diversification and inter-individuality.

Fetal programming of overweight through the microbiome: boys are disproportionately affected

Maternal and childhood obesity in pregnancy are worrisome public health issues facing our world today. New gene sequencing methods have advanced our knowledge of the disruptive effect of birth interventions and postnatal exposures on the maturation of gut microbiota and immunity during infancy. Yet, little is known about the impact of maternal pregnancy overweight on gut microbes and related processes, and how this may affect overweight risk in offspring. To address this gap in knowledge, we surveyed human studies for evidence in children, infants and pregnant women to piece together the limited literature and generate hypotheses for future investigation. From this literature, we learned that higher Lactobacillus yet lower Bacteroides spp. colonization of gut microbiota within 3 months of birth predicted risk for infant and child overweight. The abundance of bifidobacteria and staphylococci also appeared to play a role in the association with overweight, as did infant fecal immunoglobulin A levels, glycoproteins of the gut immune system that are acquired from breast milk and produced by the infant. We proposed that pregnancy overweight influences the compositional structure of gut microbiota in infants through vertical transfer of microbiota and/or their metabolites during pregnancy, delivery and breastfeeding. Finally, we brought forward emerging evidence on sex dimorphism, as well as ethnic and geographic variation, in reported associations between maternal overweight-induced gut microbiota dysbiosis and overweight risk.

Intestinal microbiota succession and immunomodulatory consequences after introduction of Lactobacillus reuteri I5007 in neonatal piglets

Seventy-two, suckling piglets, obtained from 9 litters standardized to 8 piglets, were assigned to 1 of 3 treatments (n = 24) to compare short-term, early administration with intermittent, longer-term administration of Lactobacillus reuteri I5007. The treatments were a control (given a placebo of 0.1% peptone water from day 1 to 5) or treatments in which 1.7 × 10¹⁰ CFU L. reuteri was administrated either daily for 4 days starting on day 1 or every 4th day from day 1 to 17. Five piglets per treatment were killed at 3 time points (day 7, 14 and 21). Denaturing Gradient Electrophoresis of ileal digesta revealed an increase in the presence of L. reuteri I5007 and Clostridium lentocellum (on day 14 and 21) in the every 4th-day treatment and Actinobacillus porcinus (on day 7 and 14) in both L. reuteri treatments, while reducing the abundance of E. coli on day 21 in the every 4th-day treatment. Real-time qPCR of ileal digesta showed an increase in Bifidobacterium spp. on day 14 for both L. reuteri I5007 treatments. An increase in the concentration of lactic acid and a lower pH was observed in the first 4-day treatment on day 7 and the every 4^th day treatment on day 14. The relative abundance of mRNA for TGF-β was increased while that for IFN-γ was decreased in the mesenteric lymph nodes of piglets treated with L. reuteri every 4^th day. In conclusion, early intervention with L. reuteri increases the presence of beneficial bacteria and decreases the presence of undesirable microbes in the lower gastrointestinal tract. The changes appear to be mediated by altering the intestinal pH through lactic acid production resulting in favorable bacterial species colonization. A prolonged duration of treatment (i.e. every 4^th day) would appear to be superior to treatment only during the first 4 days.

The influence of whole grain products and red meat on intestinal microbiota composition in normal weight adults: a randomized crossover intervention trial

Intestinal microbiota is related to obesity and serum lipid levels, both risk factors for chronic diseases constituting a challenge for public health. We investigated how a diet rich in whole grain (WG) products and red meat (RM) influences microbiota. During a 10-week crossover intervention study, 20 healthy adults consumed two isocaloric diets, one rich in WG products and one high in RM. Repeatedly data on microbiota were assessed by 16S rRNA based denaturing gradient gel electrophoresis (DGGE). A blood sample and anthropometric data were collected. Mixed models and logistic regression were used to investigate effects. Microbiota showed interindividual variability. However, dietary interventions modified microbiota appearance: 8 bands changed in at least 4 participants during the interventions. One of the bands appearing after WG and one increasing after RM remained significant in regression models and were identified as Collinsella aerofaciens and Clostridium sp. The WG intervention lowered obesity parameters, while the RM diet increased serum levels of uric acid and creatinine. The study showed that diet is a component of major relevance regarding its influence on intestinal microbiota and that WG has an important role for health. The results could guide investigations of diet and microbiota in observational prospective cohort studies. Trial registration: ClinicalTrials.gov NCT01449383.

High abundance of Escherichia during the establishment of fecal microbiota in Brazilian children

The sequence of bacterial events that occurs during the colonization of the gastrointestinal tract may affect the future health of the host. A clear understanding of the colonization process of the human neonatal gut in developing countries is lacking because the few available studies were mostly performed using culture techniques. Using molecular approaches, this study analyzed the fecal microbiota of children of low socioeconomic status in São Paulo, Brazil, during their first year of life. We collected fecal samples of healthy children at 3, 6, and 12 months of life. Total DNA was extracted directly from feces, and the bacteria-specific primers 27F-1492R were used to construct 16S rRNA libraries. Clones were randomly selected and partially sequenced. The main phylogenetic groups identified at 3 months were Streptococcus, unidentified bacteria, and Escherichia. At 6 months, Escherichia remained predominant, while the unidentified bacterial population increased significantly. At 12 months, a more complex composition of fecal microbiota was observed, represented by unidentified bacteria and microorganisms found at low rates at earlier ages. The genus Escherichia remained the most abundant microorganism (34% relative abundance and 75% prevalence). Principal component analysis (PCA) revealed changes in the composition of the microbiota at 6 months and an increase of diversity at 12 months of life. Bifidobacterium was identified by quantitative PCR (qPCR) and showed a high incidence in the microbiota at 3 months. The present results corroborate the global observation of inter-individual variability with an early establishment of microbial complexity at the end of the first year of life and highlight the presence of the Escherichia as abundant in microbiota composition of this group of children.

Diffusely adherent Escherichia coli strains isolated from children and adults constitute two different populations

Background

Diffusely adherent Escherichia coli (DAEC) have been considered a diarrheagenic category of E. coli for which several potential virulence factors have been described in the last few years. Despite this, epidemiological studies involving DAEC have shown inconsistent results. In this work, two different collections of DAEC possessing Afa/Dr genes, from children and adults, were studied regarding characteristics potentially associated to virulence.

Results

DAEC strains were recovered in similar frequencies from diarrheic and asymptomatic children, and more frequently from adults with diarrhea (P < 0.01) than from asymptomatic adults. Association with diarrhea (P < 0.05) was found for SAT-positive strains recovered from children and for curli-positive strains recovered from adults. Mixed biofilms involving DAEC and a Citrobacter freundii strain have shown an improved ability to form biofilms in relation to the monocultures. Control strains have shown a greater diversity of Afa/Dr adhesins and higher frequencies of cellulose, TTSS, biofilm formation and induction of IL-8 secretion than strains from cases of diarrhea in children.

Conclusions

DAEC strains possessing Afa/Dr genes isolated from children and adults represent two different bacterial populations. DAEC strains carrying genes associated to virulence can be found as part of the normal microbiota present in asymptomatic children.