scholarly journals Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age

2019 ◽  
Vol 149 (6) ◽  
pp. 1075-1088 ◽  
Author(s):  
M Nazmul Huda ◽  
Shaikh M Ahmad ◽  
Karen M Kalanetra ◽  
Diana H Taft ◽  
Md J Alam ◽  
...  
Keyword(s):  
Vitamin A ◽  
16S Rrna Gene Sequencing ◽  
Early Infancy ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Intestinal Immunity ◽  
Microbiome Composition ◽  
Vitamin A Status ◽  
Rrna Gene Sequencing ◽  
Plasma Retinol

ABSTRACTBackgroundInfancy is a crucial period for establishing the intestinal microbiome. This process may be influenced by vitamin A (VA) status because VA affects intestinal immunity and epithelial integrity, factors that can, in turn, modulate microbiome development.ObjectivesThe aim of this study was to determine if neonatal VA supplementation (VAS) affected the abundance of Bifidobacterium, a beneficial commensal, or of Proteobacteria, a phylum containing enteric pathogens, in early (6–15 wk) or late (2 y) infancy. Secondary objectives were to determine if VAS affected the abundance of other bacterial taxa, and to determine if VA status assessed by measuring plasma retinol was associated with bacterial abundance.MethodsThree hundred and six Bangladeshi infants were randomized by sex and birthweight status (above/below median) to receive 1 VA dose (50,000 IU) or placebo within 48 h of birth. Relative abundance at the genus level and above was assessed by 16S rRNA gene sequencing. A terminal restriction fragment-length polymorphism assay was used to identify Bifidobacterium species and subspecies at 6 wk.ResultsLinear regression showed that Bifidobacterium abundance in early infancy was lower in boys (median, 1st/3rd quartiles; 0.67, 0.52/0.78) than girls (0.73, 0.60/0.80; P = 0.003) but that boys receiving VAS (0.69, 0.55/0.78) had higher abundance than boys receiving placebo (0.65, 0.44/0.77; P = 0.039). However this difference was not seen in girls (VAS 0.71, 0.54/0.80; placebo 0.75, 0.63/0.81; P = 0.25). VAS did not affect Proteobacteria abundance. Sex-specific associations were also seen for VA status, including positive associations of plasma retinol with Actinobacteria (the phylum containing Bifidobacterium) and Akkermansia, another commensal with possible health benefits, for girls in late infancy.ConclusionsBetter VA status in infancy may influence health both in infancy and later in life by promoting the establishment of a healthy microbiota. This postulated effect of VA may differ between boys and girls. This trial was registered at clinicaltrials.gov as NCT02027610.

scholarly journals Effect of Commonly Used Pediatric Antibiotics on Gut Microbial Diversity in Preschool Children in Burkina Faso: A Randomized Clinical Trial

2018 ◽  
Vol 5 (11) ◽  
Author(s):  
Catherine E Oldenburg ◽  
Ali Sié ◽  
Boubacar Coulibaly ◽  
Lucienne Ouermi ◽  
Clarisse Dah ◽  
...  
Keyword(s):  
Preschool Children ◽  
Diversity Index ◽  
Controlled Trial ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Once Daily ◽  
Microbiome Composition ◽  
Α Diversity ◽  
Rrna Gene Sequencing

Abstract Background Exposure to antibiotics may result in alterations to the composition of intestinal microbiota. However, few trials have been conducted, and observational studies are subject to confounding by indication. We conducted a randomized controlled trial to determine the effect of 3 commonly used pediatric antibiotics on the intestinal microbiome in healthy preschool children. Methods Children aged 6–59 months were randomized (1:1:1:1) to a 5-day course of 1 of 3 antibiotics, including amoxicillin (25 mg/kg/d twice-daily doses), azithromycin (10 mg/kg dose on day 1 and then 5 mg/kg once daily for 4 days), cotrimoxazole (240 mg once daily), or placebo. Rectal swabs were obtained at baseline and 5 days after the last dose and were processed using 16S rRNA gene sequencing. The prespecified primary outcome was inverse Simpson’s α-diversity index. Results Post-treatment Simpson’s diversity was significantly different across the 4 arms (P = .003). The mean Simpson’s α-diversity among azithromycin-treated children was significantly lower than in placebo-treated children (6.6; 95% confidence interval [CI], 5.5–7.8; vs 9.8; 95% CI, 8.7–10.9; P = .0001). Diversity in children treated with amoxicillin (8.3; 95% CI, 7.0–9.6; P = .09) or cotrimoxazole (8.3; 95% CI, 8.2–9.7; P = .08) was not significantly different than placebo. Conclusions Azithromycin affects the composition of the pediatric intestinal microbiome. The effect of amoxicillin and cotrimoxazole on microbiome composition was less clear. Clinical Trials Registration clinicaltrials.gov NCT03187834.

scholarly journals Changes in the Intestinal Microbiome during a Multispecies Probiotic Intervention in Compensated Cirrhosis

Nutrients ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1874 ◽  
Author(s):  
Angela Horvath ◽  
Marija Durdevic ◽  
Bettina Leber ◽  
Katharina di Vora ◽  
Florian Rainer ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Controlled Trial ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Beneficial Effects ◽  
Compensated Cirrhosis ◽  
Gut Barrier Function ◽  
Probiotic Treatment

Probiotics have been used in trials to therapeutically modulate the gut microbiome and have shown beneficial effects in cirrhosis. However, their effect on the microbiome of cirrhosis patients is not fully understood yet. Here, we tested the effects of a multispecies probiotic on microbiome composition in compensated cirrhosis. The gut microbiome composition of 58 patients with compensated cirrhosis from a randomized controlled trial who received a daily dose of multispecies probiotics or placebo for six months was analysed by 16S rRNA gene sequencing. Microbiome composition of patients who received probiotics was enriched with probiotic strains and the abundance of Faecalibacterium prausnitzii, Syntrophococcus sucromutans, Bacteroides vulgatus, Alistipes shahii and a Prevotella species was increased in the probiotic group compared to the placebo group. Patients who had microbiome changes in response to probiotic treatment also showed a significant increase in neopterin and a significant decrease in faecal zonulin levels after intervention, which was not observed in placebo-treated patients or patients with unchanged microbiome compositions. In conclusion, multispecies probiotics may enrich the microbiome of compensated cirrhotic patients with probiotic bacteria during a six-month intervention and beneficially change the residential microbiome and gut barrier function.

scholarly journals The Vibrio cholerae T6SS is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome

2021 ◽  
Author(s):  
Paul Breen ◽  
Andrew D. Winters ◽  
Kevin R. Theis ◽  
Jeffrey H. Withey
Keyword(s):  
Vibrio Cholerae ◽  
Model Organism ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Model Organisms ◽  
Rrna Gene ◽  
Composition And Structure ◽  
Aquatic Microbes ◽  
Host Microbe Interactions ◽  
Rrna Gene Sequencing

Zebrafish ( Danio rerio ) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae , an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was essential for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.

scholarly journals Dietary sphinganine is selectively assimilated by members of the gut microbiome

2020 ◽  
Author(s):  
Min-Ting Lee ◽  
Henry H. Le ◽  
Elizabeth L. Johnson
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Dietary Lipids ◽  
Rrna Gene ◽  
Bioactive Components ◽  
Microbiome Composition ◽  
Metabolic Products ◽  
Comparative Metabolomics ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

AbstractFunctions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remain largely unknown. A class of lipids known as sphingolipids are bioactive components of most foods and are produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we use a click-chemistry based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne – SAA) into the gut microbial community (Click). Identification of microbe and SAA-specific metabolic products was achieved by fluorescence-based sorting of SAA containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together this approach, Click-Sort-Seq-Spec (ClickSSS), revealed that SAA-assimilation was nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice showed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activity via Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. Therefore, ClickSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

scholarly journals Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing

2020 ◽  
Vol 61 (4) ◽  
pp. 593-605
Author(s):  
Filippo Cendron ◽  
Giovanni Niero ◽  
Gabriele Carlino ◽  
Mauro Penasa ◽  
Martino Cassandro
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Fecal Bacteria ◽  
Fecal Microbiome ◽  
Alpha And Beta Diversity ◽  
Microbiome Composition ◽  
Lactating Cows ◽  
Holstein Friesian ◽  
Rrna Gene Sequencing

AbstractThe aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.

scholarly journals Effect of a Laminarin Rich Macroalgal Extract on the Caecal and Colonic Microbiota in the Post-Weaned Pig

Marine Drugs ◽  
2020 ◽  
Vol 18 (3) ◽  
pp. 157 ◽  
Author(s):  
Stafford Vigors ◽  
John V O’Doherty ◽  
Ruth Rattigan ◽  
Mary J McDonnell ◽  
Gaurav Rajauria ◽  
...  
Keyword(s):  
Feed Intake ◽  
Volatile Fatty Acids ◽  
Control Diet ◽  
Average Daily Gain ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
The Impact ◽  
Negative Relationships

Dietary supplementation with 300 ppm of a laminarin rich macroalgal extract reduces post-weaning intestinal dysfunction in pigs. A comprehensive analysis of the impact of laminarin on the intestinal microbiome during this period is essential to inform on the mode of action of this bioactivity. The objective of this study was to evaluate the effects of supplementing the diet of newly weaned pigs with 300 ppm of a laminarin rich extract, on animal performance, volatile fatty acids, and the intestinal microbiota using 16S rRNA gene sequencing. Pigs fed the laminarin-supplemented diet had higher average daily feed intake, growth rate, and body weight compared to pigs fed the control diet (p < 0.05). Pigs fed the laminarin-supplemented diet had reduced abundance of OTUs assigned to Enterobacteriaceae and increased abundance of OTUs assigned to the genus Prevotella (p < 0.05) compared to pigs fed the control diet. Enterobacteriaceae had negative relationships (p < 0.05) with average daily feed intake (ADFI), average daily gain (ADG), and butyric acid concentrations. In contrast, Prevotellaceae were positively correlated (p < 0.05) with ADFI, ADG, total VFA, acetic, propionic, butyric acids, and negatively correlated with isovaleric acid. Hence supplementation with a laminarin enriched extract potentially improves performance during the post-weaning period by promoting the proliferation of bacterial taxa such as Prevotella that favourably enhance nutrient digestion while reducing the load of potentially pathogenic bacterial taxa including Enterobacteriaceae.

scholarly journals Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ryan R. Cook ◽  
Jennifer A. Fulcher ◽  
Nicole H. Tobin ◽  
Fan Li ◽  
David J. Lee ◽  
...  
Keyword(s):  
Public Health Problem ◽  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Rrna Gene ◽  
People Living With Hiv ◽  
Major Public Health Problem ◽  
Microbiome Composition ◽  
Rrna Gene Sequencing ◽  
Sex With Men ◽  
Living With Hiv

Abstract Methamphetamine (MA) use is a major public health problem in the United States, especially among people living with HIV (PLWH). Many MA-induced neurotoxic effects are mediated by inflammation and gut microbiota may play a role in this process, yet the effects of MA on the microbiome have not been adequately explored. Therefore, we performed 16S rRNA gene sequencing on rectal swab samples from 381 men who have sex with men, 48% of whom were PLWH and 41% of whom used MA. We compared microbiome composition between MA users and non-users while testing for potential interactions with HIV and controlling for numerous confounders using inverse probability of treatment weighting. We found that MA use explained significant variation in overall composition (R2 = 0.005, p = 0.008) and was associated with elevated Finegoldia, Parvimonas, Peptoniphilus, and Porphyromonas and reduced Butyricicoccus and Faecalibacterium, among others. Genera including Actinomyces and Streptobacillus interacted with HIV status, such that they were increased in HIV+ MA users. Finegoldia and Peptoniphilus increased with increasing frequency of MA use, among others. In summary, MA use was associated with a microbial imbalance favoring pro-inflammatory bacteria, including some with neuroactive potential and others that have previously been associated with poor HIV outcomes.

scholarly journals Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

2020 ◽  
pp. jlr.RA120000950 ◽  
Author(s):  
Min-Ting Lee ◽  
Henry H Le ◽  
Elizabeth L Johnson
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Dietary Lipids ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Bioorthogonal Labeling ◽  
Comparative Metabolomics ◽  
Metabolic Activities ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.

scholarly journals Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis

2020 ◽  
Author(s):  
Maureen A. Carey ◽  
Gregory L. Medlock ◽  
Masud Alam ◽  
Mamun Kabir ◽  
Md Jashim Uddin ◽  
...  
Keyword(s):  
Diarrheal Disease ◽  
16S Rrna Gene Sequencing ◽  
Fold Change ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
Random Forest Classification ◽  
Forest Classification ◽  
Microbiome Profile ◽  
Rrna Gene Sequencing

ABSTRACTBackgroundThe protozoan parasites in the Cryptosporidium genus cause both acute diarrheal disease and subclinical (i.e. non-diarrheal) disease. It is unclear if the microbiota can influence the manifestation of diarrhea during a Cryptosporidium infection.MethodsTo characterize the role of the gut microbiota in diarrheal cryptosporidiosis, the microbiome composition of both diarrheal and surveillance Cryptosporidium-positive fecal samples was evaluated using 16S rRNA gene sequencing. Additionally, the microbiome composition prior to infection was examined to test whether a preexisting microbiome profile could influence the Cryptosporidium infection phenotype.ResultsFecal microbiome composition was associated with diarrheal symptoms at two timepoints. Megasphaera was significantly less abundant in diarrheal samples when compared to subclinical samples at the time of Cryptosporidium detection (log2(fold change) = -4.3, p=10−10) and prior to infection (log2(fold change) = -2.0, p=10−4). Random forest classification also identified Megasphaera abundance in the pre- and post-exposure microbiota.as predictive of a subclinical infection.ConclusionsMicrobiome composition broadly, and specifically low Megasphaera abundance, was associated with diarrheal symptoms prior to and at the time of Cryptosporidium detection. This observation suggests that the gut microenvironment may play a role in determining the severity of a Cryptosporidium infection.SummaryMegasphaera abundance in the stool of Bangladeshi infants is associated with the development of diarrhea upon infection with the Cryptosporidium parasite.

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