Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT

Probiotic Lactobacillus rhamnosus HN001 given in early life has been shown to reduce infant eczema risk, but its effect on gut microbiota development has not been quantitatively and functionally examined. The aim of this study was to investigate the impact of early life probiotic exposure on the composition and functional capacity of infant gut microbiota from birth to 2 years considering the effects of age, delivery mode, antibiotics, pets and eczema. We performed shotgun metagenomic sequencing analysis of 650 infant faecal samples, collected at birth, 3, 12, and 24 months, as part of a randomised, controlled, 3-arm trial assessing the effect of L. rhamnosus HN001, Bifidobacterium animalis subsp. lactis HN019 supplementation on eczema development in 474 infants. There was a 50% reduced eczema risk in the HN001 probiotic group compared to placebo. Both mothers (from 35 weeks gestation until 6 months post-partum if breastfeeding) and infants (from birth to 2 years) received either a placebo or one of two probiotics, L. rhamnosus HN001 (6×109 cfu), or B. animalis subsp. lactis HN019 (9×109 cfu). L. rhamnosus HN001 probiotic supplementation was associated with increased overall glycerol-3 phosphate transport capacity and enrichment of L. rhamnosus. There were no other significant changes in infant gut microbiota composition or diversity. Increased capacity to transport glycerol-3-phosphate was positively correlated with relative abundance of L. rhamnosus. Children who developed eczema had gut microbiota with increased capacity for glycosaminoglycan degradation and flagellum assembly but had no significant differences in microbiota composition or diversity. Early life HN001 probiotic use is associated with both increased L. rhamnosus and increased infant gut microbiota functional capacity to transport glycerol-3 phosphate. The mechanistic relationship of such functional alteration in gut microbiota with reduced eczema risk and long-term health merits further investigation.

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Early-Life Development of the Bifidobacterial Community in the Infant Gut

International Journal of Molecular Sciences ◽

10.3390/ijms22073382 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3382

Author(s):

Silvia Saturio ◽

Alicja M. Nogacka ◽

Marta Suárez ◽

Nuria Fernández ◽

Laura Mantecón ◽

...

Keyword(s):

Gut Microbiota ◽

Gestational Age ◽

Early Life ◽

Feeding Habits ◽

Its Region ◽

23S Rrna ◽

Delivery Mode ◽

Short And Long Term ◽

Quantitative Changes ◽

The Impact

The establishment of the gut microbiota poses implications for short and long-term health. Bifidobacterium is an important taxon in early life, being one of the most abundant genera in the infant intestinal microbiota and carrying out key functions for maintaining host-homeostasis. Recent metagenomic studies have shown that different factors, such as gestational age, delivery mode, or feeding habits, affect the gut microbiota establishment at high phylogenetic levels. However, their impact on the specific bifidobacterial populations is not yet well understood. Here we studied the impact of these factors on the different Bifidobacterium species and subspecies at both the quantitative and qualitative levels. Fecal samples were taken from 85 neonates at 2, 10, 30, 90 days of life, and the relative proportions of the different bifidobacterial populations were assessed by 16S rRNA–23S rRNA internal transcribed spacer (ITS) region sequencing. Absolute levels of the main species were determined by q-PCR. Our results showed that the bifidobacterial population establishment is affected by gestational age, delivery mode, and infant feeding, as it is evidenced by qualitative and quantitative changes. These data underline the need for understanding the impact of perinatal factors on the gut microbiota also at low taxonomic levels, especially in the case of relevant microbial populations such as Bifidobacterium. The data obtained provide indications for the selection of the species best suited for the development of bifidobacteria-based products for different groups of neonates and will help to develop rational strategies for favoring a healthy early microbiota development when this process is challenged.

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Association of gut microbiota composition and function with an aged rat model of senile osteoporosis using 16S rRNA and metagenomic sequencing analysis

Aging ◽

10.18632/aging.103293 ◽

2020 ◽

Vol 12 (11) ◽

pp. 10795-10808 ◽

Cited By ~ 2

Author(s):

Sicong Ma ◽

Jinhong Qin ◽

Yongqiang Hao ◽

Lingjie Fu

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Rat Model ◽

Sequencing Analysis ◽

Metagenomic Sequencing ◽

Microbiota Composition ◽

Aged Rat ◽

Senile Osteoporosis ◽

And Function ◽

Gut Microbiota Composition

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The Central Role of the Gut Microbiota in Chronic Inflammatory Diseases

Journal of Immunology Research ◽

10.1155/2014/689492 ◽

2014 ◽

Vol 2014 ◽

pp. 1-12 ◽

Cited By ~ 79

Author(s):

Caroline Marcantonio Ferreira ◽

Angélica Thomaz Vieira ◽

Marco Aurelio Ramirez Vinolo ◽

Fernando A. Oliveira ◽

Rui Curi ◽

...

Keyword(s):

Immune System ◽

Gut Microbiota ◽

Intestinal Microbiota ◽

Immune Cell ◽

Inflammatory Diseases ◽

Sequencing Analysis ◽

Metagenomic Sequencing ◽

Microbiota Composition ◽

Chronic Inflammatory Diseases ◽

Commensal Microbiota

The commensal microbiota is in constant interaction with the immune system, teaching immune cells to respond to antigens. Studies in mice have demonstrated that manipulation of the intestinal microbiota alters host immune cell homeostasis. Additionally, metagenomic-sequencing analysis has revealed alterations in intestinal microbiota in patients suffering from inflammatory bowel disease, asthma, and obesity. Perturbations in the microbiota composition result in a deficient immune response and impaired tolerance to commensal microorganisms. Due to altered microbiota composition which is associated to some inflammatory diseases, several strategies, such as the administration of probiotics, diet, and antibiotic usage, have been utilized to prevent or ameliorate chronic inflammatory diseases. The purpose of this review is to present and discuss recent evidence showing that the gut microbiota controls immune system function and onset, development, and resolution of some common inflammatory diseases.

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Early Life Microbiota Colonization at Six Months of Age: A Transitional Time Point

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.590202 ◽

2021 ◽

Vol 11 ◽

Author(s):

Benedetta Raspini ◽

Mirco Vacca ◽

Debora Porri ◽

Rachele De Giuseppe ◽

Francesco Maria Calabrese ◽

...

Keyword(s):

Gut Microbiota ◽

Early Life ◽

Maternal Body Mass Index ◽

Microbiota Composition ◽

Fecal Samples ◽

Breastfed Infants ◽

Gestational Weight ◽

Significant Difference ◽

The Impact ◽

Older Siblings

BackgroundEarly life gut microbiota is involved in several biological processes, particularly metabolism, immunity, and cognitive neurodevelopment. Perturbation in the infant’s gut microbiota increases the risk for diseases in early and later life, highlighting the importance of understanding the connections between perinatal factors with early life microbial composition. The present research paper is aimed at exploring the prenatal and postnatal factors influencing the infant gut microbiota composition at six months of age.MethodsGut microbiota of infants enrolled in the longitudinal, prospective, observational study “A.MA.MI” (Alimentazione MAmma e bambino nei primi MIlle giorni) was analyzed. We collected and analyzed 61 fecal samples at baseline (meconium, T0); at six months of age (T2), we collected and analyzed 53 fecal samples. Samples were grouped based on maternal and gestational weight factors, type of delivery, type of feeding, time of weaning, and presence/absence of older siblings. Alpha and beta diversities were evaluated to describe microbiota composition. Multivariate analyses were performed to understand the impact of the aforementioned factors on the infant’s microbiota composition at six months of age.ResultsDifferent clustering hypotheses have been tested to evaluate the impact of known metadata factors on the infant microbiota. Neither maternal body mass index nor gestational weight gain was able to determine significant differences in infant microbiota composition six months of age. Concerning the type of feeding, we observed a low alpha diversity in exclusive breastfed infants; conversely, non-exclusively breastfed infants reported an overgrowth of Ruminococcaceae and Flavonifractor. Furthermore, we did not find any statistically significant difference resulting from an early introduction of solid foods (before 4 months of age). Lastly, our sample showed a higher abundance of clostridial patterns in firstborn babies when compared to infants with older siblings in the family.ConclusionOur findings showed that, at this stage of life, there is not a single factor able to affect in a distinct way the infants’ gut microbiota development. Rather, there seems to be a complex multifactorial interaction between maternal and neonatal factors determining a unique microbial niche in the gastrointestinal tract.

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A fructo-oligosaccharide prebiotic is well-tolerated in adults undergoing allogeneic hematopoietic stem cell transplantation: a phase I dose-escalation trial

10.1101/2021.04.26.21256127 ◽

2021 ◽

Author(s):

Tessa. M. Andermann ◽

Farnaz Fouladi ◽

Fiona B. Tamburini ◽

Bita Sahaf ◽

Ekaterina Tkachenko ◽

...

Keyword(s):

Gut Microbiota ◽

Phase I ◽

Cell Transplantation ◽

Gut Microbiome ◽

Metagenomic Sequencing ◽

Microbiota Composition ◽

Hematopoietic Stem ◽

The Impact ◽

Gut Microbiota Composition ◽

Reduced Intensity

AbstractBackgroundAlterations of the gut microbiota after allogeneic hematopoietic cell transplantation (allo-HCT) are a key factor in the development of transplant-related complications such as graft-versus-host disease (GVHD). Interventions that preserve the gut microbiome hold promise to improve HCT-associated morbidity and mortality. Murine models demonstrate that prebiotics such as fructo-oligosaccharides (FOS) may increase gut levels of short-chain fatty acids (SCFAs) such as butyrate, and consequently induce proliferation of immunomodulatory CD4+ FOXP3+ T-regulatory cells (Tregs), that impact GVHD risk.MethodsWe conducted a pilot Phase I trial to assess the investigate the maximum tolerated dose of FOS in patients undergoing reduced-intensity (RIC) allo-HCT (n=15) compared to concurrent controls (n=16). We administered FOS starting at pretransplant conditioning and continuing for a total of 21 days. We characterized the gut microbiome using shotgun metagenomic sequencing, measured stool SCFAs using LC-MS, and determined peripheral T-cell concentrations using CyTOF.ResultsWe found that FOS was safe and well-tolerated at 10g per day without significant adverse effects in patients undergoing reduced-intensity conditioning allo-HCT. Community-level gut microbiota composition was significantly different on the day of transplant (day 0) between patients receiving FOS compared to concurrent controls, however FOS-associated alterations of the gut microbiota were not sustained after transplant. Although the impact of FOS was fleeting, transplantation itself impacted a substantial number of taxa over time. In our small pilot trial, no significant differences were observed in gut microbial metabolic pathways, stool SCFAs, or in peripheral Tregs although Tregs trended higher in those patients who received FOS. Early alterations in gut microbiota composition in those receiving FOS are especially intriguing although it remains unclear what impact this has on outcomes following transplantation and larger studies are required to investigate the use of prebiotics in HCT recipients.ConclusionsFOS is well-tolerated at 10g per day in patients undergoing RIC allo-HCT.

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Lactobacillus rhamnosus Probio-M9 Improves the Quality of Life in Stressed Adults by Gut Microbiota

Foods ◽

10.3390/foods10102384 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2384

Author(s):

Yan Zheng ◽

Zhongjie Yu ◽

Wenyi Zhang ◽

Tiansong Sun

Keyword(s):

Quality Of Life ◽

Gut Microbiota ◽

Life Quality ◽

Lactobacillus Rhamnosus ◽

Metagenomic Sequencing ◽

Before And After ◽

Probiotic Intervention ◽

Physiological Quality ◽

The Impact

To evaluate the effect of the probiotic, Lactobacillus rhamnosus Probio-M9 (Probio-M9), on the quality of life in stressed adults. Methods: Twelve postgraduate student volunteers were recruited. Six volunteers received oral Probio-M9 for 21 days, while the remaining six received a placebo instead. Fecal samples were collected from the volunteers before and after the intervention. Metagenomic sequencing, nontargeted metabonomics, and quality-of-life follow-up questionnaires were used to evaluate the impact of Probio-M9 consumption on the gut microbiota and life quality of the volunteers. Results: Probio-M9 improved the psychological and physiological quality-of-life symptoms significantly in stressed adults (p < 0.05). The probiotic intervention was beneficial in increasing and maintaining the diversity of gut microbiota. The abundance of Barnesiella and Akkermansia increased in the probiotics group. The feature metabolites of pyridoxamine, dopamine, and 5-hydroxytryptamine (5-HT) were positively correlated with Barnesiella and Akkermansia levels, which might be why the mental state of the volunteers in the probiotic group improved after taking Probio-M9. Conclusions: We identified that oral Probio-M9 can regulate the stability of gut microbiota and affect the related beneficial metabolites, thereby affecting the quality of life (QoL) of stressed adults. Probio-M9 might improve the psychological and physiological quality of life in stressed adults via the gut-brain axis pathway. The causal relationship should be further explored in future studies.

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Metformin Affects Gut Microbiota Composition and Diversity Associated with Amelioration of Dextran Sulfate Sodium-Induced Colitis in Mice

Frontiers in Pharmacology ◽

10.3389/fphar.2021.640347 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhiyi Liu ◽

Wangdi Liao ◽

Zihan Zhang ◽

Ruipu Sun ◽

Yunfei Luo ◽

...

Keyword(s):

Gut Microbiota ◽

Dextran Sulfate ◽

Dextran Sulfate Sodium ◽

Bacterial Community Composition ◽

Intestinal Flora ◽

Sequencing Analysis ◽

Metagenomic Sequencing ◽

Metformin Treatment ◽

Microbiota Composition ◽

Beneficial Effects

Background: Inflammatory bowel disease (IBD) is an increasingly common and globally emergent immune-mediated disorder. The etiology of IBD is complex, involving multiple factors such as immune dysregulation, environmental factors, genetic mutations, and microbiota dysbiosis, exacerbated by a lack of effective clinical therapies. Recently, studies hypothesized that dysbiosis of intestinal flora might participate in the onset of IBD. Metformin is widely used to treat type 2 diabetes and has shown beneficial effects in mouse models of IBD, although its underlying mechanisms remain poorly understood. Accumulating studies found that metformin shows beneficial effects for diabetes by affecting microbiota composition. This study explores possible regulatory effects of metformin on intestinal microecology during treatment for IBD.Methods: Inflammation was induced using 3% Dextran Sulfate Sodium (DSS) solution to generate mice models of IBD. Metformin treatments were assayed by measuring body weights and colon lengths of mice and H&E staining to observe histological effects on colon tissue structures. Changes in bacterial community composition and diversity-related to IBD and metformin treatment were assessed by high-throughput metagenomic sequencing analysis.Results: Metformin administration significantly ameliorated body weight loss, inhibited colon shrinking, and contributed to preserving the integrity of colon histological structures. The gut microbiota profiles revealed that the biodiversity of intestinal flora lost during inflammation was restored under metformin treatment. Metformin administration was also associated with decreased pathogenic Escherichia shigella and increased abundance of Lactobacillus and Akkermansia.Conclusion: Metformin appears to induce anti-inflammatory effects, thus ameliorating colitis symptoms, concurrent with enrichment for beneficial taxa and restored microbial diversity, suggesting a viable strategy against IBD.

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Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis

Animals ◽

10.3390/ani11061825 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1825

Author(s):

Mohamed Zeineldin ◽

Ameer Megahed ◽

Benjamin Blair ◽

Brian Aldridge ◽

James Lowe

Keyword(s):

Sequencing Analysis ◽

Metagenomic Sequencing ◽

Post Intervention ◽

Gastrointestinal Microbiome ◽

Health And Wellbeing ◽

Suckling Piglets ◽

And Function ◽

Changes Over Time ◽

And Control ◽

The Impact

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

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Antibiotics at birth and later antibiotic courses: effects on gut microbiota

Pediatric Research ◽

10.1038/s41390-021-01494-7 ◽

2021 ◽

Author(s):

Sofia Ainonen ◽

Mysore V Tejesvi ◽

Md. Rayhan Mahmud ◽

Niko Paalanne ◽

Tytti Pokka ◽

...

Keyword(s):

Gut Microbiota ◽

Control Group ◽

List Type ◽

Antibiotic Exposure ◽

Microbiota Composition ◽

Long Term Effects ◽

The Impact ◽

Antibiotic Courses ◽

Gut Microbiota Composition

Abstract Background Intrapartum antibiotic prophylaxis (IAP) is widely used, but the evidence of the long-term effects on the gut microbiota and subsequent health of children is limited. Here, we compared the impacts of perinatal antibiotic exposure and later courses of antibiotic courses on gut microbiota. Methods This was a prospective, controlled cohort study among 100 vaginally delivered infants with different perinatal antibiotic exposures: control (27), IAP (27), postnatal antibiotics (24), and IAP and postnatal antibiotics (22). At 1 year of age, we performed next-generation sequencing of the bacterial 16S ribosomal RNA gene of fecal samples. Results Exposure to the perinatal antibiotics had a clear impact on the gut microbiota. The abundance of the Bacteroidetes phylum was significantly higher in the control group, whereas the relative abundance of Escherichia coli was significantly lower in the control group. The impact of the perinatal antibiotics on the gut microbiota composition was greater than exposure to later courses of antibiotics (28% of participants). Conclusions Perinatal antibiotic exposure had a marked impact on the gut microbiota at the age of 1 year. The timing of the antibiotic exposure appears to be the critical factor for the changes observed in the gut microbiota. Impact Infants are commonly exposed to IAP and postnatal antibiotics, and later to courses of antibiotics during the first year of life. Perinatal antibiotics have been associated with an altered gut microbiota during the first months of life, whereas the evidence regarding the long-term impact is more limited. Perinatal antibiotic exposure had a marked impact on the infant’s gut microbiota at 1 year of age. Impact of the perinatal antibiotics on the gut microbiota composition was greater than that of the later courses of antibiotics at the age of 1 year.

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