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 Vibrio cholerae Infection Induces Strain Specific Modulation of the 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 ◽  
Microbial Profile ◽  
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. Zebrafish contain a core ( i.e. , consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic, and can be significantly altered to due external factors. Zebrafish are particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae . As an intestinal pathogen, V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. Members of the resident intestinal microbial community likely must be reduced or eliminated by V. cholerae in order for colonization, and subsequent disease, to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few have examined how a V. cholerae infection alters the resident intestinal microbiome. In this study, 16S rRNA gene sequencing was utilized to investigate how five genetically diverse V. cholerae strains alter the intestinal microbiome following an infection. We found that V. cholerae colonization induced significant changes in the zebrafish intestinal microbiome. Notably, changes in the microbial profile were significantly different from each other, based on the particular strain of V. cholerae used to infect zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiota to enable colonization and specific microbes that are targeted depend on the V. cholerae genotype.

scholarly journals Effects of Vibrio cholerae infection and colonization on the zebrafish intestinal microbiome

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Paul Breen ◽  
Andrew Winters ◽  
Kevin Theis ◽  
Jeffrey Withey
Keyword(s):  
Microbial Community ◽  
Vibrio Cholerae ◽  
Model Organism ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Model Organisms ◽  
Rrna Gene ◽  
Microbial Profile ◽  
Aquatic Microbes ◽  
Host Microbe Interactions

Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic, and can be significantly altered to due external factors. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae needs to colonize the intestine of an exposed host for any type of pathogenicity to occur. It is suspected that members of the resident intestinal microbial community need to be eliminated by V. cholerae in order for colonization, and subsequently disease, 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 community. In this study, 16S rRNA gene sequencing was utilized to investigate how various strains of V. cholerae alter the aforementioned microbial profiles following an infection. We found that V. cholerae infection and subsequent colonization induced significant changes in the zebrafish intestinal microbiome, with specific members of the microbial community targeted. Additional salient differences to the microbial profile were observed based on the particular strain of V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae causes significant modulation to the zebrafish intestinal microbiome in order for infection and subsequent disease to occur.

scholarly journals Dynamic changes of the fecal bacterial community in dairy cows during early lactation

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shuai Huang ◽  
Shoukun Ji ◽  
Feiran Wang ◽  
Jie Huang ◽  
Gibson Maswayi Alugongo ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Early Lactation ◽  
Lactating Cows ◽  
Composition And Structure ◽  
Dietary Transition ◽  
Fecal Bacterial Community ◽  
Rrna Gene Sequencing

Abstract The dynamics of the community structure and composition of the dairy cow fecal bacterial communities during early lactation is unclear, therefore this study was conducted to characterize the fecal bacterial communities in dairy cows during early lactation using 16S rRNA gene sequencing. Feces were sampled from 20 healthy fresh Holstein dairy cows on day 1 (Fresh1d group) and day 14 (Fresh14d group) after calving. After calving, cows were fed the same fresh diet. The dominant phyla Firmicutes and Proteobacteria were decreased (P ≤ 0.01) with lactating progress and phyla Bacteroidetes were increased (P = 0.008) with lactating progress and dietary transition. At family level, the predominant families were Ruminococcaceae (35.23%), Lachnospiraceae (11.46%), Rikenellaceae (10.44%) and Prevotellaceae (6.89%). A total of 14 genera were different between fecal samples from Fresh1d and Fresh14d, included the predominant genera, such as Ruminococcaceae_UCG-005 (P = 0.008), Rikenellaceae_RC9_gut_group (P = 0.043) and Christensenellaceae_R-7_group (P = 0.008). All fecal bacterial communities shared members of the genera Ruminococcaceae_UCG-005, Bacteroides and Rikenellaceae_RC9_gut_group. These findings help to improve our understanding of the composition and structure of the fecal microbial community in fresh cows and may provide insight into bacterial adaptation time and dietary in lactating cows.

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 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 Dissection of the gut microbiota in mothers and children with chronic Trichuris trichiura infection in Pemba Island, Tanzania

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Hongliang Chen ◽  
Matteo Mozzicafreddo ◽  
Elisa Pierella ◽  
Vanessa Carletti ◽  
Angela Piersanti ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Neglected Tropical Diseases ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Pemba Island ◽  
Life Years ◽  
Degrading Bacteria ◽  
Mothers And Children ◽  
Rrna Gene Sequencing

Abstract Background Soil-transmitted helminthiases are important neglected tropical diseases that result in a notably high number of disability-adjusted life years worldwide. Characterizing the interactions between the human intestinal microbiome and helminths is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance. Methods We recruited and obtained fecal samples from 32 pairs of mothers and children on Pemba Island and monitored their intestinal microbiota using 16S rRNA gene sequencing. Results We observed that microbial changes occur in the gut microbiota of infected mothers and children. Some short-chain fatty acid (SCFA)-producing bacteria and carbohydrate-degrading bacteria exhibited lower abundance in the infected individuals. Potentially pathogenic Campylobacter and proinflammatory Methanobrevibacter in infected mothers and opportunistic Enterococcus in infected children exhibited greater abundance. Conclusions Our findings could reveal the microbiota profiling in T. trichiura-infected individuals, indicate the potential roles of key microbiota in the host and aid to the development of novel strategies to control T. trichiura infection. Graphic abstract

scholarly journals Effect of Pepper-Containing Diets on the Diversity and Composition of Gut Microbiome of Drosophila melanogaster

2020 ◽  
Vol 21 (3) ◽  
pp. 945 ◽  
Author(s):  
Marleny Garcia-Lozano ◽  
Joshua Haynes ◽  
Carlos Lopez-Ortiz ◽  
Purushothaman Natarajan ◽  
Yadira Peña-Garcia ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Host Genotype ◽  
Microbial Composition ◽  
Potential Health ◽  
Gastrointestinal Microbiome ◽  
Composition And Structure ◽  
Rrna Gene Sequencing

One of the greatest impacts on the gastrointestinal microbiome is diet because the host and microbiome share the same food source. In addition, the effect of diet can diverge depending on the host genotype. Diets supplemented with phytochemicals found in peppers might cause shifts in the microbiome. Thus, understanding how these interactions occur can reveal potential health implications associated with such changes. This study aims to explore the gut microbiome of different Drosophila genetic backgrounds and the effects of dietary pepper treatments on its composition and structure. We analyzed the gut microbiomes of three Drosophila melanogaster genetic backgrounds (Canton-S, Oregon-RC, and Berlin-K) reared on control and pepper-containing diets (bell, serrano, and habanero peppers). Results of 16S rRNA gene sequencing revealed that the variability of Drosophila gut microbiome can be driven mainly by genetic factors. When the abundance of these communities is considered, pepper-containing diets also appear to have an effect. The most relevant change in microbial composition was the increment of Lactobacillaceae and Acetobacteraceae abundance in the pepper-containing diets in comparison with the controls in Oregon-RC and Berlin-K. Regression analysis demonstrated that this enhancement was associated with the content of phenolic compounds and carotenoids of the peppers utilized in this study; specifically, to the concentration of β-carotene, β-cryptoxanthin, myricetin, quercetin, and apigenin.

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 The development of gut microbiota in ostriches and its association with juvenile growth

2018 ◽  
Author(s):  
Elin Videvall ◽  
Se Jin Song ◽  
Hanna M. Bensch ◽  
Maria Strandh ◽  
Anel Engelbrecht ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
16S Rrna Gene Sequencing ◽  
Model Organisms ◽  
Rrna Gene ◽  
Juvenile Growth ◽  
Adult Fitness ◽  
Yolk Absorption ◽  
Rrna Gene Sequencing ◽  
Extinction Events

AbstractThe development of gut microbiota during ontogeny in vertebrates is emerging as an important process influencing physiology, immune system, health, and adult fitness. However, we have little knowledge of how the gut microbiome is colonised and develops in non-model organisms, and to what extent microbial diversity and specific taxa influence changes in fitness-related traits. Here, we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiota in juvenile ostriches (Struthio camelus; n = 71) over their first three months of life, during which time a five-fold difference in weight was observed. We found a gradual increase in microbial diversity with age, an overall convergence in community composition among individuals, multiple colonisation and extinction events, and major taxonomic shifts coinciding with the cessation of yolk absorption. In addition, we discovered significant but complex associations between juvenile growth and microbial diversity, and identified distinct bacterial groups that had positive (Bacteroidaceae) and negative (Enterobacteriaceae, Enterococcaceae, Lactobacillaceae) correlations with the growth of individuals at specific ages. These results have broad implications for our understanding of the development of gut microbiota and its association with juvenile growth.

scholarly journals Gut Microbiota Profile in Patients with Type 1 Diabetes Based on 16S rRNA Gene Sequencing: A Systematic Review

2020 ◽  
Vol 2020 ◽  
pp. 1-11 ◽  
Author(s):  
He Zhou ◽  
Xue Zhao ◽  
Lin Sun ◽  
Yujia Liu ◽  
You Lv ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Case Control ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Case Control Studies ◽  
Rrna Gene Sequencing

The gut microbiota has been presumed to have a role in the pathogenesis of type 1 diabetes (T1D). Significant changes in the microbial composition of T1D patients have been reported in several case-control studies. This study is aimed at systematically reviewing the existing literature, which has investigated the alterations of the intestinal microbiome in T1D patients compared with healthy controls (HCs) using 16S ribosomal RNA-targeted sequencing. The databases of MEDLINE, EMBASE, Web of Science, and the Cochrane Library were searched until April 2019 for case-control studies comparing the composition of the intestinal microbiome in T1D patients and HCs based on 16S rRNA gene sequencing techniques. The Newcastle-Ottawa Scale was used to assess the methodological quality. Ten articles involving 260 patients with T1D and 276 HCs were included in this systematic review. The quality scores of all included studies were 6–8 points. In summary, a decreased microbiota diversity and a significantly distinct pattern of clustering with regard to β-diversity were observed in T1D patients when compared with HCs. At the phylum level, T1D was characterised by a reduced ratio of Firmicutes/Bacteroidetes in the structure of the gut community, although no consistent conclusion was reached. At the genus or species level, T1D patients had a reduced abundance of Clostridium and Prevotella compared with HCs, whereas Bacteroides and Ruminococcus were found to be more enriched in T1D patients. This systematic review identified that there is a close association between the gut microbiota and development of T1D. Moreover, gut dysbiosis might be involved in the pathogenesis of T1D, although the causative role of gut microbiota remains to be established. Further well-controlled prospective studies are needed to better understand the role of the intestinal microbiome in the pathogenesis of T1D, which may help explore novel microbiota-based strategies to prevent and treat T1D.

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