Development Of Microbiota Research Articles

The difference of intestinal microbiota composition between Lantang and Landrace newborn piglets

BackgroundThe early development of intestinal microbiota plays a fundamental role in host health and development. To investigate the difference in the intestinal microbial composition between Lantang and Landrace newborn piglets, we amplified and sequenced the V3-V4 region of 16 S rRNA gene in jejunal microbiota of Lantang and landrace newborn.ResultsThe findings revealed that the dominant phyla in the jejunum of Lantang piglets were Firmicutes, Actinobacteria and Bacteroidetes, while the dominant phyla of Landrace is Proteobacteria and Fusobacteria. Specifically, Corynebacterium_1, Lactobacillus, Rothia, Granulicatella, Corynebacteriales_unclassified, Corynebacterium, Globicatella and Actinomycetales_unclassified were found to be the dominant genera of Lantang group, while Clostridium_sensu_stricto_1, Escherichia-Shigella, Actinobacillus and Bifidobacterium were the dominant genera of Landrace. Based on the functional prediction of bacteria, we found that bacterial communities from Lantang samples had a significantly greater abundance pathways of fatty acid synthesis, protein synthesis, DNA replication, recombination, repair and material transport across membranes, while the carrier protein of pathogenic bacteria was more abundant in Landrace samples.ConclusionsOverall, there was a tremendous difference in the early intestinal flora composition between Landang and Landrace piglets, which was related to the breed characteristics and may be one of the reasons affecting the growth characteristics. However, more further extensive studies should be included to reveal the underlying relationship between early intestinal flora composition in different breeds and pig growth characteristics.

Lentinula edodes Cultured Extract and Rouxiella badensis subsp. acadiensis (Canan SV-53) Intake Alleviates Immune Deregulation and Inflammation by Modulating Signaling Pathways and Epigenetic Mechanisms.

Puberty is a critical developmental period of life characterized by marked physiological changes, including changes in the immune system and gut microbiota development. Exposure to inflammation induced by immune stressors during puberty has been found to stimulate central inflammation and lead to immune disturbance at distant sites from the gut; however, its enduring effects on gut immunity are not well explored. Therefore, in this study, we used a pubertal lipopolysaccharides (LPS)-induced inflammation mouse model to mimic pubertal exposure to inflammation and dysbiosis. We hypothesized that pubertal LPS-induced inflammation may cause long-term dysfunction in gut immunity by enduring dysregulation of inflammatory signaling and epigenetic changes, while prebiotic/probiotic intake may mitigate the gut immune system deregulation later in life. To this end, four-week-old female Balb/c mice were fed prebiotics/probiotics and exposed to LPS in the pubertal window. To better decipher the acute and enduring immunoprotective effects of biotic intake, we addressed the effect of treatment on interleukin (IL)-17 signaling related-cytokines and pathways. In addition, the effect of treatment on gut microbiota and epigenetic alterations, including changes in microRNA (miRNA) expression and DNA methylation, were studied. Our results revealed a significant dysregulation in selected cytokines, proteins, and miRNAs involved in key signaling pathways related to IL-17 production and function, including IL-17A and F, IL-6, IL-1β, transforming growth factor-β (TGF-β), signal transducer and activator of transcription-3 (STAT3), p-STAT3, forkhead box O1 (FOXO1), and miR-145 in the small intestine of adult mice challenged with LPS during puberty. In contrast, dietary interventions mitigated the lasting adverse effects of LPS on gut immune function, partly through epigenetic mechanisms. A DNA methylation analysis demonstrated that enduring changes in gut immunity in adult mice might be linked to differentially methylated genes, including Lpb, Rorc, Runx1, Il17ra, Rac1, Ccl5, and Il10, involved in Th17 cell differentiation and IL-17 production and signaling. In addition, prebiotic administration prevented LPS-induced changes in the gut microbiota in pubertal mice. Together, these results indicate that following a healthy diet rich in prebiotics and probiotics is an optimal strategy for programming immune system function in the critical developmental windows of life and controlling inflammation later in life.

Alterations of milk oligosaccharides in mothers with gestational diabetes mellitus impede colonization of beneficial bacteria and development of RORγt+ Treg cell-mediated immune tolerance in neonates

ABSTRACT Gestational diabetes mellitus (GDM) is an increasing public health concern that significantly increases the risk of early childhood allergic diseases. Altered maternal milk glycobiome may strongly affect gut microbiota and enteric-specific Treg cell-mediated development of immune tolerance in GDM infants. In this study, we found that, compared with healthy Chinese mothers, mothers with GDM had significantly lower levels of total and specific human milk oligosaccharides (HMOs) in their colostrum that subsequently increased with extension of lactation. This alteration in HMO profiles significantly delayed colonization of Lactobacillus and Bifidobacterium spp. in their breast-fed infants, resulting in a distinct gut microbial structure and metabolome. Further experiments in GDM mouse models indicated that decreased contents of milk oligosaccharides, mainly 3ʹ-sialyllactose (3ʹ-SL), in GDM maternal mice reduced colonization of bacteria, such as L. reuteri and L. johnsonii, in the neonatal gut, which impeded development of RORγt+ regulatory T (Treg) cell-mediated immune tolerance. Treatment of GDM neonates with 3ʹ-SL, Lactobacillus reuteri (L. reuteri) and L. johnsonii promoted the proliferation of enteric Treg cells and expression of transcription factor RORγt, which may have contributed to compromising ovalbumin (OVA)-induced allergic responses. In vitro experiments showed that 3ʹ-SL, metabolites of L. johnsonii, and lysates of L. reuteri stimulated differentiation of mouse RORγt+ Treg cells through multiple regulatory effects on Toll-like receptor, MAPK, p53, and NOD-like receptor signaling pathways. This study provides new ideas for the development of gut microbiota and immune tolerance in GDM newborns.

The Effect of Maternal Probiotic or Synbiotic Supplementation on Sow and Offspring Gastrointestinal Microbiota, Health, and Performance.

The increasing prevalence of antimicrobial-resistant pathogens has prompted the reduction in antibiotic and antimicrobial use in commercial pig production. This has led to increased research efforts to identify alternative dietary interventions to support the health and development of the pig. The crucial role of the GIT microbiota in animal health and performance is becoming increasingly evident. Hence, promoting an improved GIT microbiota, particularly the pioneer microbiota in the young pig, is a fundamental focus. Recent research has indicated that the sow's GIT microbiota is a significant contributor to the development of the offspring's microbiota. Thus, dietary manipulation of the sow's microbiota with probiotics or synbiotics, before farrowing and during lactation, is a compelling area of exploration. This review aims to identify the potential health benefits of maternal probiotic or synbiotic supplementation to both the sow and her offspring and to explore their possible modes of action. Finally, the results of maternal sow probiotic and synbiotic supplementation studies are collated and summarized. Maternal probiotic or synbiotic supplementation offers an effective strategy to modulate the sow's microbiota and thereby enhance the formation of a health-promoting pioneer microbiota in the offspring. In addition, this strategy can potentially reduce oxidative stress and inflammation in the sow and her offspring, enhance the immune potential of the milk, the immune system development in the offspring, and the sow's feed intake during lactation. Although many studies have used probiotics in the maternal sow diet, the most effective probiotic or probiotic blends remain unclear. To this extent, further direct comparative investigations using different probiotics are warranted to advance the current understanding in this area. Moreover, the number of investigations supplementing synbiotics in the maternal sow diet is limited and is an area where further exploration is warranted.

Functional proteins in breast milk and their correlation with the development of the infant gut microbiota: a study of mother-infant pairs.

Proteins in breast milk play an important role in the growth and development of infants. This study aims to explore the correlation between functional proteins in breast milk and the infant gut microbiota. Twenty-three mothers and their infants were enrolled and breast milk samples and infant fecal samples were collected. Breast milk protein content was determined by UPLC-MS/MS, and 16S rRNA sequencing was employed to analyze the gut microbiota of infant. The results indicated that the secretory immunoglobulin A (sIgA) content in breast milk was positively correlated with the abundance of Veillonella parvula. The κ-casein content was positively correlated with the abundance of Clostridium butyricum. The osteopontin (OPN) and lactalbumin contents were positively correlated with the abundance of Parabacteroides distasonis at 42 days. Functional pathway analysis showed that the OPN and κ-casein contents in breast milk were significantly correlated with amino acid, pyruvate, propionic acid, linoleic acid, and alpha-linolenic acid metabolic pathways in early life. The results of this study suggest that specific proteins in breast milk can influence the abundance of certain gut microbes in infants, playing an important role in early immune and metabolic development.

Temporal stability and community assembly mechanisms in healthy broiler cecum.

In recent years, there has been an unprecedented advancement in in situ analytical approaches that contribute to the mechanistic understanding of microbial communities by explicitly incorporating ecology and studying their assembly. In this study, we have analyzed the temporal profiles of the healthy broiler cecal microbiome from day 3 to day 35 to recover the stable and varying components of microbial communities. During this period, the broilers were fed three different diets chronologically, and therefore, we have recovered signature microbial species that dominate during each dietary regime. Since broilers were raised in multiple pens, we have also parameterized these as an environmental condition to explore microbial niches and their overlap. All of these analyses were performed in view of different parameters such as body weight (BW-mean), feed intake (FI), feed conversion ratio (FCR), and age (days) to link them to a subset of microbes that these parameters have a bearing upon. We found that gut microbial communities exhibited strong and statistically significant specificity for several environmental variables. Through regression models, genera that positively/negatively correlate with the bird's age were identified. Some short-chain fatty acids (SCFAs)-producing bacteria, including Izemoplasmatales, Gastranaerophilales, and Roseburia, have a positive correlation with age. Certain pathogens, such as Escherichia-Shigella, Sporomusa, Campylobacter, and Enterococcus, negatively correlated with the bird's age, which indicated a high disease risk in the initial days. Moreover, the majority of pathways involved in amino acid biosynthesis were also positively correlated with the bird's age. Some probiotic genera associated with improved performance included Oscillospirales; UCG-010, Shuttleworthia, Bifidobacterium, and Butyricicoccaceae; UCG-009. In general, predicted antimicrobial resistance genes (piARGs) contributed at a stable level, but there was a slight increase in abundance when the diet was changed. To the best of the authors' knowledge, this is one of the first studies looking at the stability, complexity, and ecology of natural broiler microbiota development in a temporal setting.

The cause and effect of gut microbiota in development of inflammatory disorders of the breast

BackgroundInflammatory disorders of the breast (IDB) damages the interests of women and children and hinders the progress of global health seriously. Several studies had offered clues between gut microbiota (GM) and inflammatory disorders of the breast (IDB). The gut–mammary gland axis also implied a possible contribution of the GM to IDB. However, the causality between them is still elusive.MethodsThe data of two-sample Mendelian randomization (MR) study related to the composition of GM (n = 18,340) and IDB (n = 177,446) were accessed from openly available genome-wide association studies (GWAS) database. As the major analytical method, inverse variance weighted (IVW) was introduced and several sensitive analytical methods were conducted to verify results.ResultsInverse variance weighted revealed Eubacterium rectale group (OR = 1.87, 95% CI: 1.02–3.43, p = 4.20E−02), Olsenella (OR = 1.29, 95% CI: 1.02–1.64, p = 3.30E−02), Ruminiclostridium-6 (OR = 1.53, 95% CI: 1.08–2.14, p = 1.60E−02) had an anti-protective effect on IDB. Peptococcus (OR = 0.75, 95% CI: 0.60–0.94, p = 1.30E−02) had a protective effect on IDB. The results were credible through a series of test.ConclusionsWe revealed causality between IDB and GM taxa, exactly including Ruminiclostridium-6, Eubacterium rectale group, Olsenella and Peptococcus. These genera may become novel biomarkers and supply new viewpoint for probiotic treatment. However, these findings warrant further test owing to the insufficient evidences.

Effects of a novel, non-invasive pre-hatch application of probiotic for broilers on development of cecum microbiota and production performance

BackgroundProbiotics are used in the broiler industry to increase production performance. Most often a probiotic is applied by mixing it in the feed, but studies have shown that earlier application may be advantageous. Therefore, in ovo application where the probiotic is administrated into the egg before hatch has been investigated as an alternative application method. However, in ovo application may impact hatchability negatively and may not be feasible at all hatcheries. The purpose of this study was to investigate the effect of a novel non-invasive method for mass application before hatch. The probiotic (E. faecium 669) was applied as a single dose by spray on the unhatched eggs and production performance and development of the cecal microbiota until slaughter was compared with a control flock. Through 16S rRNA sequencing of cecal samples from 25 broilers at day 7, 21 and 37 we compared the microbiota composition and richness for each group. The study was repeated for additional recording of production performance and re-isolation of the probiotic E. faecium from the intestine.ResultsIn both trials the probiotic E. faecium could be re-isolated from the yolk sac and intestine at hatch and at day 7. Broilers in the probiotic treated groups had a higher performance in terms of bodyweight at day 34 and European production efficiency factor. Finally, a significant reduction of first-week and overall mortality was observed in the probiotic group in the first trial. Based on 16S rRNA profiling, significant differences in alpha diversity were found exclusively at day 37. Estimation of beta diversities, however, identified significant differences in microbiota composition between the control and probiotic group at day 7, 21 and 37.ConclusionThe probiotic E. faecium strain successfully colonized broilers before/during hatch after a single spray application at day 18 of incubation. Positive effects of the probiotic were observed in multiple production parameters, including reduced mortality in trial 1, and microbiota analyses indicate significantly different microbiota compositions throughout the experimental phase. Taken together, the novel low-tech mass administration of E. faecium (669) may be considered a feasible strategy for improvements of production parameters in broiler production.

Trackability of proteins from probiotic Bifidobacterium spp. in the gut using metaproteomics.

Beneficial effects of Bifidobacterium spp. on gut microbiota development and infant health have been reported earlier. Therefore, supplementation of infant formulas with probiotic bifidobacteria, as well as prebiotics stimulating bifidobacterial growth, has been proposed. Here, we studied the faecal microbiome of infants supplemented with specialized nutrition, of which some received a standard amino acid-based formula (AAF) and others an AAF with a specific mixture of prebiotics and a probiotic (synbiotics) using metaproteomics and 16S rRNA gene sequencing. Faecal samples were taken at baseline, as well as after 6 and 12 months fed with the specialized formula. The aim was to compare microbial differences between infants treated with the standard AAF and those who received the additional synbiotics. Our findings show that infants who received AAF with synbiotics have significantly higher levels of Bifidobacteriaceae DNA as well as significantly increased levels of Coriobacteriaceae proteins, over time. Moreover, at visit 12 months higher levels of some bifidobacterial carbohydrate-active enzymes, known to metabolize oligosaccharides, were observed in the synbiotic group compared to the non-synbiotic group. The results indicate that the synbiotics provided in our study are trackable in faecal samples on the DNA and protein level during the intervention period.

Characterization and Correlation of Dominant Microbiota and Flavor Development in Different Post-Mortem Processes of Beef.

Post-mortem aging could enhance the unique flavors of beef via several biochemical pathways. The microbiota is one of the important factors in the flavor development of aging beef, but their potential relationship has rarely been studied. This study characterized the apparent meat quality, flavor profiles, and microbial communities of beef during the different post-mortem processes, followed by the investigation of the correlations between the dominant microbiota and key volatile compounds. The results showed that wet-aged beef has a higher product yield and more stable color than dry-aged beef, as evidenced by the significantly lower value of aging loss and discoloration (ΔE). According to the odor activity value, 11 out of 65 compounds were categorized as aroma-active components, and 9 of them, including 1-pentanol, 1-octen-3-ol, hexanal, nonanal, heptanal, octanal, 2-nonenal, (E)-, 2-octenal, (E)- and 2-decenal, (E)-, were enriched in beef wet-aged for 7 d. Significant variances were found in the microbial communities of different aging beef. Of these, 20 microbiota (with 10 bacterial and 10 fungal genera) were recognized as the dominant genus. Partial least squares regression combined with a correlation network model revealed that five microbial genera, including Trichosporon, Prauserella, Rhodotorula, Malassezia, and Corynebacterium, constituted the functional microbiota responsible for flavor formation in aging beef and were positively associated with ≥7 key volatile compounds (p < 0.05, |ρ| > 0.7). This study suggests that the application of wet aging within 7 d on beef is better for meat quality and provides novel insights into the mechanisms of flavor formation in post-mortem aging beef via functional microbiota.

Comparison of 16S rRNA gene sequencing microbiota among children with serological IgE-mediated food hypersensitivity.

We hypothesized that specific food hypersensitivity (FH) in children is linked to specific gut microbiota. The aim of our study was to quantify and evaluate differences in gut microbial composition among children with different IgE-mediated FH. Children (n = 81) aged 18 to 36 months were enrolled, fecal samples of 57 children with FH and 24 healthy children were evaluated using next-generation sequencing. Individual microbial diversity and composition were analyzed via targeting the 16 S rRNA gene hypervariable V3-V5 regions. Children with IgE-mediated FH (in milk, egg white, soy) had significantly lower gut microbiota diversity and richness than healthy children. Children with IgE-mediated FH exhibited relatively high abundances of Firmicutes and relative underrepresentation of the phylum Bacteroidetes. We observed significant increases in relative abundances of Ruminococcaceae, Clostridiaceae, and Erysipelotrichaceae (p < 0.01, compared to control) in children with milk hypersensitivity and of Clostridiaceae and Erysipelotrichaceae (p < 0.01) in children with peanut hypersensitivity. We also found significant increases in the numbers of Clostridiaceae, Lachnospiraceae and Pasteurellaceae (p < 0.01) in children with egg white hypersensitivity. These findings identify early evidence of different gut microbiota development/ differentiation in children with food hypersensitivity. Specific food hypersensitivities may be associated with compositional changes in intestinal microbiota. These findings identify early evidence of different gut microbiota development/differentiation in children with food hypersensitivity. We built a gut microbial profile that could identify toddlers at risk for food hypersensitivity. Children with enriched Firmicutes (phylum) with partial different families may be associated with food hypersensitivity. Enriched family Clostridiaceae, Ruminococcaceae, Lachnospiraceae, or Erysipelotrichaceae in gut microbiota may be associated with specific food hypersensitivities (such as milk, egg white, peanut) in children.

The contribution of maternal oral, vaginal, and gut microbiota to the developing offspring gut

There is limited understanding of how the microbiota colonizing various maternal tissues contribute to the development of the neonatal gut microbiota (GM). To determine the contribution of various maternal microbiotic sites to the offspring microbiota in the upper and lower gastrointestinal tract (GIT) during early life, litters of mice were sacrificed at 7, 9, 10, 11, 12, 14, and 21 days of age, and fecal and ileal samples were collected. Dams were euthanized alongside their pups, and oral, vaginal, ileal, and fecal samples were collected. This was done in parallel using mice with either a low-richness or high-richness microbiota to assess the consistency of findings across multiple microbial compositions. Samples were analyzed using 16S rRNA amplicon sequencing. The compositional similarity between pup and dam samples were used to determine the contribution of each maternal source to the composition of the neonate fecal and ileal samples at each timepoint. As expected, similarity between neonate and maternal feces increased significantly over time. During earlier time-points however, the offspring fecal and ileal microbiotas were closer in composition to the maternal oral microbiota than other maternal sites. Prominent taxa contributed by the maternal oral microbiota to the neonate GM were supplier-dependent and included Lactobacillus spp., Streptococcus spp., and a member of the Pasteurellaceae family. These findings align with the microbial taxa reported in infant microbiotas, highlighting the translatability of mouse models in this regard, as well as the dynamic nature of the GM during early life.

Infant gut microbiota colonization: influence of prenatal and postnatal factors, focusing on diet.

Maternal microbiota forms the first infant gut microbial inoculum, and perinatal factors (diet and use of antibiotics during pregnancy) and/or neonatal factors, like intra partum antibiotics, gestational age and mode of delivery, may influence microbial colonization. After birth, when the principal colonization occurs, the microbial diversity increases and converges toward a stable adult-like microbiota by the end of the first 3-5 years of life. However, during the early life, gut microbiota can be disrupted by other postnatal factors like mode of infant feeding, antibiotic usage, and various environmental factors generating a state of dysbiosis. Gut dysbiosis have been reported to increase the risk of necrotizing enterocolitis and some chronic diseases later in life, such as obesity, diabetes, cancer, allergies, and asthma. Therefore, understanding the impact of a correct maternal-to-infant microbial transfer and a good infant early colonization and maturation throughout life would reduce the risk of disease in early and late life. This paper reviews the published evidence on early-life gut microbiota development, as well as the different factors influencing its evolution before, at, and after birth, focusing on diet and nutrition during pregnancy and in the first months of life.

Transmission of Alzheimer's disease-associated microbiota dysbiosis and its impact on cognitive function: evidence from mice and patients.

Spouses of Alzheimer's disease (AD) patients are at a higher risk of developing incidental dementia. However, the causes and underlying mechanism of this clinical observation remain largely unknown. One possible explanation is linked to microbiota dysbiosis, a condition that has been associated with AD. However, it remains unclear whether gut microbiota dysbiosis can be transmitted from AD individuals to non-AD individuals and contribute to the development of AD pathogenesis and cognitive impairment. We, therefore, set out to perform both animal studies and clinical investigation by co-housing wild-type mice and AD transgenic mice, analyzing microbiota via 16S rRNA gene sequencing, measuring short-chain fatty acid amounts, and employing behavioral test, mass spectrometry, site-mutations and other methods. The present study revealed that co-housing between wild-type mice and AD transgenic mice or administrating feces of AD transgenic mice to wild-type mice resulted in AD-associated gut microbiota dysbiosis, Tau phosphorylation, and cognitive impairment in the wild-type mice. Gavage with Lactobacillus and Bifidobacterium restored these changes in the wild-type mice. The oral and gut microbiota of AD patient partners resembled that of AD patients but differed from healthy controls, indicating the transmission of microbiota. The underlying mechanism of these findings includes that the butyric acid-mediated acetylation of GSK3β at lysine 15 regulated its phosphorylation at serine 9, consequently impacting Tau phosphorylation. Pending confirmative studies, these results provide insight into a potential link between the transmission of AD-associated microbiota dysbiosis and development of cognitive impairment, which underscore the need for further research in this area.

Development of Gut Microbiota in the First 1000 Days after Birth and Potential Interventions.

The first 1000 days after birth represent a critical window for gut microbiome development, which is essential for immune system maturation and overall health. The gut microbiome undergoes major changes during this period due to shifts in diet and environment. Disruptions to the microbiota early in life can have lasting health effects, including increased risks of inflammatory disorders, autoimmune diseases, neurological disorders, and obesity. Maternal and environmental factors during pregnancy and infancy shape the infant gut microbiota. In this article, we will review how maintaining a healthy gut microbiome in pregnancy and infancy is important for long-term infant health. Furthermore, we briefly include fungal colonization and its effects on the host immune function, which are discussed as part of gut microbiome ecosystem. Additionally, we will describe how potential approaches such as hydrogels enriched with prebiotics and probiotics, gut microbiota transplantation (GMT) during pregnancy, age-specific microbial ecosystem therapeutics, and CRISPR therapies targeting the gut microbiota hold potential for advancing research and development. Nevertheless, thorough evaluation of their safety, effectiveness, and lasting impacts is crucial prior to their application in clinical approach. The article emphasizes the need for continued research to optimize gut microbiota and immune system development through targeted early-life interventions.

Breastfeeding and the major fermentation metabolite lactate determine occurrence of Peptostreptococcaceae in infant feces

ABSTRACT Previous studies indicated an intrinsic relationship between infant diet, intestinal microbiota composition and fermentation activity with a strong focus on the role of breastfeeding on microbiota composition. Yet, microbially formed short-chain fatty acids acetate, propionate and butyrate and other fermentation metabolites such as lactate not only act as substrate for bacterial cross-feeding and as mediators in microbe–host interactions but also confer antimicrobial activity, which has received considerably less attention in the past research. It was the aim of this study to investigate the nutritional–microbial interactions that contribute to the development of infant gut microbiota with a focus on human milk oligosaccharide (HMO) fermentation. Infant fecal microbiota composition, fermentation metabolites and milk composition were analyzed from 69 mother-infant pairs of the Swiss birth cohort Childhood AlleRgy nutrition and Environment (CARE) at three time points depending on breastfeeding status defined at the age of 4 months, using quantitative microbiota profiling, HPLC-RI and 1H-NMR. We conducted in vitro fermentations in the presence of HMO fermentation metabolites and determined the antimicrobial activity of lactate and acetate against major Clostridiaceae and Peptostreptococcaceae representatives. Our data show that fucosyllactose represented 90% of the HMOs present in breast milk at 1- and 3-months post-partum with fecal accumulation of fucose, 1,2-propanediol and lactate indicating fermentation of HMOs that is likely driven by Bifidobacterium. Concurrently, there was a significantly lower absolute abundance of Peptostreptococcaceae in feces of exclusively breastfed infants at 3 months. In vitro, lactate inhibited strains of Peptostreptococcaceae. Taken together, this study not only identified breastfeeding dependent fecal microbiota and metabolite profiles but suggests that HMO-derived fermentation metabolites might exert an inhibitory effect against selected gut microbes.

Dynamic distribution of gut microbiota in posthatching chicks and its relationship with average daily gain

The colonization and development of gut microbiota are essential for the health and growth of chicks after hatching. However, the colonization and prevalence of gut microbiota have not been well characterized, and knowledge of which microbes and their relationship with average daily gain in chicks is still limited. This study characterized the dynamic succession of microbiota in the intestinal tract of chicks and investigated its relationship with daily weight gain. A total of 121 fecal samples across 7 time points from d 0 to 10 posthatching were collected from 19 chicks randomly selected from 1,950 chicks. Using 16S rRNA gene sequencing examined microbial composition of fecal samples. The observed species index of alpha diversity increased with age, gradually achieving stability at 3 d of age. The microbiota of chicks after hatching was primarily Clostridium_sensu_stricto_1 (34.49%), and its relative abundance diminishes with age. In contrast, Lactobacillus had a low relative abundance in the first 2 d after hatching and gradually increased with age. Predicted functional capacities found that the microbiota of early-stage posthatching (d 0 and 1 after hatching) was involved in metabolism, including amino acid metabolism, metabolism of cofactors and vitamins, and nitrogen metabolism. However, at the later stage posthatching (from d 3-10 after hatching), the intestinal microbial function was involved in carbohydrate metabolism, amino acid metabolism, cell growth and death, and methane metabolism. It was identified that 47 operational taxonomic units were associated with average daily gain of chicks, 12 of which were annotated with Lactobacillus and significantly positive associated with average daily gain. In addition, Clostridium_sensu_stricto_1 was significantly negatively associated with average daily gain. Taken together, we characterized the dynamic successions of intestinal microbiota in hatching chicks. The intestinal microbiota of chicks has an impact on the host average daily gain. Our findings should be instrumental in improving local chick production.

The correlation of the intestinal with pharyngeal microbiota in early neonates.

The gut-lung axis has long been recognized as an important mechanism affecting intestinal and lung immunity. Still, few studies have examined the correlation between the intestinal and pharyngeal microbiota in early neonates, especially when feeding patterns are one of the main drivers of microbiota development. To explore the composition and function of intestinal and pharyngeal microbiota and to analyze the effect of limited formula feeding on the initial microbiota colonization in early full-term neonates, we characterized the stool and oropharyngeal microbiota of 20 healthy full-term newborns sampled on days 0 and 5-7 after birth using 16S rRNA gene sequencing. Based on the sequencing results, a comparison was made of the compositions and functions of the intestinal and oropharyngeal microbiota for analysis. At the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most abundant in both niches. At the genus level, the species of pioneer bacteria were rich in the intestine and oropharynx but low in abundance on day 0. On days 5-7, Bifidobacterium (25.40%) and Escherichia-Shigella (22.16%) were dominant in the intestine, while Streptococcus (38.40%) and Staphylococcus (23.13%) were dominant in the oropharynx. There were eight core bacteria genera in the intestine and oropharynx on days 5-7, which were Bifidobacterium, Escherichia-Shigella, Staphylococcus, Streptococcus, Bacteroides, Parabacteroides, Rothia, and Acinetobacter. As indicated by PICRUSt analysis, on days 5-7, the intestinal microbiota was more predictive than the oropharyngeal microbiota in transcription, metabolism, cell motility, cellular processes and signaling, and organismal system function in the KEGG pathway. Compared to exclusive breastfeeding, limited formula feeding (40-60%) had no significant effect on the neonatal intestinal and oropharyngeal microbiota composition during the initial colonization period. Our results suggest that the initial colonization of microbiota is closely related to the ecological niche environment in the intestine and oropharynx, with their core microbiota being closely correlated. We found that early limited formula feeding could not significantly affect the initial colonization of microbiota in the intestine and oropharynx.

Conserved Covarying Gut Microbial Network in Preterm Infants and Childhood Growth During the First 5 Years of Life: A Prospective Cohort Study

BackgroundLongitudinally conserved microbe-microbe interactions may provide insights to understand the complex dynamic system of early-life gut microbiota among preterm infants. ObjectivesWe aimed to profile the covarying network of gut microbiota among preterm infants and investigate its potential influence on host growth (2–5 y). MethodsWe collected time-series stool samples (n = 717 from children and n = 116 from mothers) among 51 preterm and 51 full-term infants from birth up to 5 y of age and among 53 mothers. The included infants underwent time-series measurements of early-life gut microbiota (0–5 y) and growth (2–5 y) from June 2014 to April 2017. The covarying taxa that exhibited consistent covariation from day 1 to year 5 were defined as conserved features in the development of gut microbiota. Childrens’ height-for-age z score (HAZ) and weight-for-age z score were calculated according to World Health Organization Child Growth Standards. ResultsWe observed distinct dynamic patterns of both microbial alpha and beta diversity comparing preterm infants with full-term controls during the very early stage (<3 mo). Moreover, we identified a covarying network containing 10 taxa as a conserved gut microbial feature of these preterm infants from birth to 5 y old. This covarying network was distinctive between preterm and full-term infants before 3 mo of age (P < 0.001) and tended to be similar as the infants grew up. Several covarying taxa of the network during early life (<3 mo) were associated with childhood growth (2–5 y) (eg, Clostridium_sensu_stricto_1 with HAZ, β = -0.32, q < 0.01), and the human milk feeding duration was a main modulating factor. ConclusionsPreterm born children possess conserved and distinct covarying microbiota during very early life, which may have a profound influence on their growth later in life.This trial was registered at clinicaltrials.gov as NCT03373721.

Characterization of the upper respiratory tract microbiota in Chilean asthmatic children reveals compositional, functional, and structural differences.

Around 155 million people worldwide suffer from asthma. In Chile, the prevalence of this disease in children is around 15% and has a high impact in the health system. Studies suggest that asthma is caused by multiple factors, including host genetics, antibiotic use, and the development of the airway microbiota. Here, we used 16S rRNA high-throughput sequencing to characterize the nasal and oral mucosae of 63 asthmatic and 89 healthy children (152 samples) from Santiago, Chile. We found that the nasal mucosa was dominated by a high abundance of Moraxella, Dolosigranulum, Haemophilus, Corynebacterium, Streptococcus, and Staphylococcus. In turn, the oral mucosa was characterized by a high abundance of Streptococcus, Haemophilus, Gemella, Veillonella, Neisseria, and Porphyromonas. Our results showed significantly (P < 0.001) lower alpha diversity and an over-abundance of Streptococcus (P < 0.01) in nasal samples from asthmatics compared to samples from healthy subjects. Community structure, as revealed by co-occurrence networks, showed different microbial interactions in asthmatic and healthy subjects, particularly in the nasal microbiota. The networks revealed keystone genera in each body site, including Prevotella, Leptotrichia, and Porphyromonas in the nasal microbiota, and Streptococcus, Granulicatella, and Veillonella in the oral microbiota. We also detected 51 functional pathways differentially abundant on the nasal mucosa of asthmatic subjects, although only 13 pathways were overrepresented in the asthmatic subjects (P < 0.05). We did not find any significant differences in microbial taxonomic (composition and structure) and functional diversity between the oral mucosa of asthmatic and healthy subjects. This study explores for the first time the relationships between the upper respiratory airways bacteriome and asthma in Chile. It demonstrates that the nasal cavity of children from Santiago harbors unique bacterial communities and identifies potential taxonomic and functional biomarkers of pediatric asthma.