Structural changes in gut microbiome after Ramadan fasting: a pilot study

2020 ◽  
Vol 11 (3) ◽  
pp. 227-233
Author(s):  
C. Ozkul ◽  
M. Yalinay ◽  
T. Karakan
Keyword(s):  
Microbial Community ◽  
Pilot Study ◽  
Structural Changes ◽  
Bacterial Species ◽  
Shannon Index ◽  
Microbial Community Analysis ◽  
Intermittent Fasting ◽  
Microbial Composition ◽  
Ramadan Fasting ◽  
Significant Difference

It has been largely accepted that dietary changes have an effect on gut microbial composition. In this pilot study we hypothesised that Ramadan fasting, which can be considered as a type of time-restricted feeding may lead to changes in gut microbial composition and diversity. A total of 9 adult subjects were included in the study. Stool samples were collected before (baseline) and at the end of the Ramadan fasting (after 29 days). Following the construction of an 16S rRNA amplicon library, the V4 region was sequenced using the Illumina Miseq platform. Microbial community analysis was performed using the QIIME program. A total of 27,521 operational taxonomic units (OTUs) with a 97% similarity were determined in all of the samples. Microbial richness was significantly increased after Ramadan according to observed OTU results (P=0.016). No significant difference was found in terms of Shannon index or phylogenetic diversity metrics of alpha diversity. Microbial community structure was significantly different between baseline and after Ramadan samples according to unweighted UniFrac analysis (P=0.025). LEfSe analysis revealed that Butyricicoccus, Bacteroides, Faecalibacterium, Roseburia, Allobaculum, Eubacterium, Dialister and Erysipelotrichi were significantly enriched genera after the end of Ramadan fasting. According to random forest analysis, the bacterial species most affected by the Ramadan fasting was Butyricicoccus pullicaecorum. Despite this is a pilot study with a limited sample size; our results clearly revealed that Ramadan fasting, which represents an intermittent fasting regime, leads to compositional changes in the gut microbiota.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study

Nutrients ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 1272
Author(s):  
Boopalan Ramasamy ◽  
Fabien Magne ◽  
Sujit Kumar Tripathy ◽  
Giriprasad Venugopal ◽  
Diptasree Mukherjee ◽  
...  
Keyword(s):  
Vitamin D ◽  
Pilot Study ◽  
Knee Osteoarthritis ◽  
Vitamin D Deficiency ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Serum Vitamin ◽  
Core Microbiome ◽  
Serum Vitamin D ◽  
Significant Difference

Background: Few preclinical studies have shown that Knee osteoarthritis (KOA) is linked to gut microbiome dysbiosis and chronic inflammation. This pilot study was designed to look at the gut microbiome composition in KOA patients and normal individuals with or without vitamin D deficiency (VDD, serum vitamin D <30 ng/mL). Methods: This pilot study was conducted prospectively in 24 participants. The faecal samples of all the participants were taken for DNA extraction. The V3-V4 region of 16s rRNA was amplified, and the library was prepared and sequenced on the Illumina Miseq platform. Results: The mean (±SD) age was 45.5 (±10.2) years with no defined comorbidities. Of 447 total Operational Taxonomic Units (OTUs), a differential abundance of 16 nominally significant OTUs between the groups was observed. Linear discriminate analysis (LEfSe) revealed a significant difference in bacteria among the study groups. Pseudobutyrivibrio and Odoribacter were specific for VDD, while Parabacteroides, Butyricimonas and Gordonibacter were abundant in the KOA_VDD group, and Peptococcus, Intestimonas, Delftia and Oribacterium were abundant in the KOA group. About 80% of bacterial species were common among different groups and hence labelled as core bacterial species. However, the core microbiome of KOA and VDD groups were not seen in the KOA_VDD group, suggesting that these bacterial groups were affected by the interaction of the KOA and VDD factors. Conclusion: Parabacteroides, Butyricimonas, Pseudobutyrivibrio, Odoribacter and Gordonibacter are the predominant bacteria in vitamin D deficient patients with or without KOA. Together these results indicate an association between the gut microbiome, vitamin D and knee osteoarthritis.

A study of the correlation between chalazion and intestinal flora in chinese children

2020 ◽  
Author(s):  
Yuanyue Cui ◽  
Lei Song ◽  
Xie Li ◽  
Ting Qiu ◽  
Jing Jin ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Diversity Index ◽  
Bacterial Species ◽  
Intestinal Flora ◽  
Meibomian Gland ◽  
Control Group ◽  
Healthy Children ◽  
Gut Flora ◽  
Microbial Composition ◽  
Significant Difference

Abstract BackgroundChalazion is a chronic inflammatory granuloma of the meibomian gland formed on the basis of the obstruction of the meibomian gland drainage duct and the retention of secretions. It is one of the most common clinically eye diseases in children. Chronic inflammation of the meibomian glands is responsible for this disease, and the gut flora is thought to be involved in the inflammatory process. In this study, we investigated the relationship between intestinal microbial composition and children's chalazion.MethodsFecal samples were collected from 21 children with chalazion and 26 healthy children. DNA was extracted from fecal stool samples and 16S rRNA sequences in the gut flora were detected by using second second-generation sequencing technology. The results were used to compare the composition of the microbiome between patients and healthy controls.ResultsAccording to Alpha Diversity and Beta Diversity analysis, we found that there was no significant difference in bacteria diversity and relative abundance between the two groups. We compared the flora of the control group and the diseased group through Lefse analysis, and screened out 11 different species. Based on the absolute abundance of species, 43 different species were selected. Anosim analysis and metastats analysis were used to compare the flora of the control group and the diseased group again. At the species level, we found that gut_metagenome and human_gut_metagenome are the common differences in species levels obtained from the above analysis. Finally, corrplot correlation analysis was performed, suggesting that gut_metagenome has a great correlation with the number, ulceration, and recurrence of chalazion in children.ConclusionsThere was no significant difference in the diversity index and relative abundance of flora in children with chalazion compared with healthy children, but there were significant differences in some bacterial species. The gut_metagenome strains identified in this study were significantly related to the growth, ulceration, and relapse of children with chalazion. It is suggested that gut_metagenome may be a microbiological indicator which is independent of clinicopathologic factors but associated with chalazion disease .* These authors have contributed equally to this work.

Microbial Community Analysis on Oxic-Settling-Anaerobic Process by Using PCR-DGGE Assay

2011 ◽  
Vol 255-260 ◽  
pp. 2934-2939 ◽  
Author(s):  
Jian Fang Wang ◽  
Qing Liang Zhao
Keyword(s):  
Microbial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Analysis ◽  
Diversity Indices ◽  
Community Diversity ◽  
Microbial Community Analysis ◽  
Organic Loading Rate ◽  
Slight Variation ◽  
Biological Phosphorus Removal ◽  
Microbial Composition

In situ sludge reduction of the oxic-settling-anaerobic (OSA) process was investigated in this study and microbial community diversity in the system was analyzed by using a PCR-denaturing gradient gel electrophoresis (DGGE) approach. Comparing to the conventional activated sludge method, the production of excessive sludge in the OSA process was shown to be efficiently reduced by 44-50 % and the organic loading rate was observed to have a slight impact on sludge yield. As demonstrated by the slight variation of Shannon diversity indices (SDI), the dominant microbial composition remained stable in the OSA sludge with the increase ofNs. About 63% of clones represented by predominant bands in the DGGE pattern were affiliated with the subclass ofb-proteobacteria. A number of bacteria in the OSA process were phylogenetically related to uncultured bacteria isolated from enhanced biological phosphorus removal (EBPR) sludge.

scholarly journals Influence of dietary components on development of the microbiota in single-stomached species

2006 ◽  
Vol 19 (1) ◽  
pp. 63-78 ◽  
Author(s):  
Eva Bauer ◽  
Barbara A Williams ◽  
Hauke Smidt ◽  
Rainer Mosenthin ◽  
Martin W. A Verstegen
Keyword(s):  
Microbial Community ◽  
Bacterial Species ◽  
Promoting Effect ◽  
Microbial Composition ◽  
Health Promoting ◽  
Carbohydrate Fermentation ◽  
Dietary Components ◽  
Growth Promoting ◽  
Fermentable Carbohydrates ◽  
Gain Access

AbstractAfter birth, development of a normal microbial community occurs gradually, and is affected by factors such as the composition of the maternal gut microbiota, the environment, and the host genome. Diet also has a direct influence, both on composition and activity of this community. This influence begins with the milk, when specific components exert their growth-promoting effect on a beneficial microbiota, thereby suppressing potential pathogens. For example, breast-fed infants compared with formula-fed babies usually have a microbial community dominated by bifidobacteria. When solid food is introduced (weaning), dramatic changes in microbial composition occur, so pathogens can gain access to the disturbed gastrointestinal (GI) ecosystem. However, use of specific dietary components can alter the composition and activity of the microbiota positively. Of all dietary components, fermentable carbohydrates seem to be most promising in terms of promoting proliferation of beneficial bacterial species. Carbohydrate fermentation results in the production of SCFA which are known for their trophic and health-promoting effects. Fermentation of proteins, on the other hand, is often associated with growth of potential pathogens, and results in production of detrimental substances including NH3and amines. In terms of the GI microbiota, lipids are often associated with the antimicrobial activity of medium-chain fatty acids and their derivatives. The present review aims to provide deeper insights into the composition and development of the neonatal GI microbiota, how this microbiota can be influenced by certain dietary components, and how this might ultimately lead to improvements in host health.

scholarly journals Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qian Wang ◽  
Xuelan Chen ◽  
Huan Hu ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Structural Changes ◽  
Dental Fluorosis ◽  
Bacterial Species ◽  
Fusobacterium Nucleatum ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Diseases

AbstractDental fluorosis is a very prevalent endemic disease. Although oral microbiome has been reported to correlate with different oral diseases, there appears to be an absence of research recognizing any relationship between the severity of dental fluorosis and the oral microbiome. To this end, we investigated the changes in oral microbial community structure and identified bacterial species associated with moderate and severe dental fluorosis. Salivary samples of 42 individuals, assigned into Healthy (N = 9), Mild (N = 14) and Moderate/Severe (M&S, N = 19), were investigated using the V4 region of 16S rRNA gene. The oral microbial community structure based on Bray Curtis and Weighted Unifrac were significantly changed in the M&S group compared with both of Healthy and Mild. As the predominant phyla, Firmicutes and Bacteroidetes showed variation in the relative abundance among groups. The Firmicutes/Bacteroidetes (F/B) ratio was significantly higher in the M&S group. LEfSe analysis was used to identify differentially represented taxa at the species level. Several genera such as Streptococcus mitis, Gemella parahaemolysans, Lactococcus lactis, and Fusobacterium nucleatum, were significantly more abundant in patients with moderate/severe dental fluorosis, while Prevotella melaninogenica and Schaalia odontolytica were enriched in the Healthy group. In conclusion, our study indicates oral microbiome shift in patients with moderate/severe dental fluorosis. We identified several differentially represented bacterial species enriched in moderate and severe fluorosis. Findings from this study suggests that the roles of these bacteria in oral health and related diseases warrant more consideration in patients with moderate and severe fluorosis.

scholarly journals Elucidating the Gut Microbiome of Colorectal Cancer: 40 Fecal Bacteria as Non-invasive Biomarkers

2020 ◽  
Author(s):  
Biao Yuan ◽  
SiPing Ma ◽  
Qingkai Meng ◽  
Tao Du ◽  
Yueyan Zhu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Early Diagnosis ◽  
Sensitivity And Specificity ◽  
Gut Microbiome ◽  
Microbial Community Analysis ◽  
Support Vector ◽  
Healthy Controls ◽  
Microbial Composition ◽  
Non Invasive ◽  
Specificity And Sensitivity

Abstract Background: Colorectal adenocarcinoma (CRC) ranks one of the 5 most lethal malignant tumors both in China and worldwide. Emerging evidences have revealed the importance of gut microbiome on CRC, thus microbial community could be termed as a potential screen for early diagnosis. Importantly, compared with the whole microbial community analysis, few numbers of bacteria genus as non-invasive biomarkers with high sensitivity and specificity causing less cost would benefit more in clinical. Methods: Here we analyzed the gut microbiome from 226 CRC patients and 156 healthy people by 16s rRNA sequencing. We analyzed the microbiome diversity between CRC patients and healthy controls. We used ExtraTrees classifier to screening the biomarkers and took SVM (Support Vector Machine) model to test the specificity and sensitivity of our biomarkers. Results: Compared with the healthy gut, the microbial composition are divergent in CRC, especially the increase of some bacteria related to CRC and the decrease of some healthy bacteria. 40 bacteria genus exhibiting high weight for the healthy and CRC microbiome classification were screened as biomarkers for CRC. In addition, the combination of 40 biomarkers and FOBT showed an outstanding sensitivity and specificity for discrimination CRC patients from healthy controls. Conclusion: The method could be used as a non-invasive method for CRC early diagnosis.

scholarly journals Overabundance of Asaia and Serratia bacteria is associated with deltamethrin insecticide susceptibiltiy in Anopheles coluzzii from Agboville, Cote d'Ivoire

2021 ◽  
Author(s):  
Bethanie Pelloquin ◽  
Mojca Kristan ◽  
Constant Edi ◽  
Anne Meiwald ◽  
Emma Clark ◽  
...  
Keyword(s):  
16S Rrna ◽  
Insecticide Resistance ◽  
Mosquito Species ◽  
Shannon Index ◽  
Malaria Vector Control ◽  
Anopheles Coluzzii ◽  
Microbial Composition ◽  
Degrading Bacteria ◽  
Significant Difference ◽  
Deltamethrin Resistance

Background: Insecticide resistance among mosquito species is now a pervasive phenomenon, which threatens to jeopardise global malaria vector control efforts. Evidence of links between the mosquito microbiota and insecticide resistance is emerging, with significant enrichment of insecticide degrading bacteria and enzymes in resistant populations. Using 16S rRNA amplicon sequencing, we characterised and compared the microbiota of Anopheles (An.) coluzzii in relation to their deltamethrin resistance and exposure profiles. Results: Comparisons between 2-3 day old deltamethrin resistant and susceptible mosquitoes, demonstrated significant differences in microbiota diversity (PERMANOVA, pseudo-F = 19.44, p=0.0015). Ochrobactrum, Lysinibacillus and Stenotrophomonas genera, each of which comprised insecticide degrading species, were significantly enriched in resistant mosquitoes. Susceptible mosquitoes had a significant reduction in alpha diversity compared to resistant individuals (Shannon index: H=13.91, q=0.0003, Faiths phylogenetic diversity: H=6.68, q=0.01), with Asaia and Serratia dominating microbial profiles. There was no significant difference in deltamethrin exposed and unexposed 5-6 day old individuals, suggesting that insecticide exposure had minimal impact on microbial composition. Serratia and Asaia were also dominant in 5-6 day old mosquitoes, regardless of exposure or phenotype, and had reduced microbial diversity compared with 2-3 day old mosquitoes. Conclusions: Our findings revealed significant alterations of An. coluzzii microbiota associated with deltamethrin resistance, highlighting the potential for identification of novel microbial markers for insecticide resistance surveillance. qPCR detection of Serratia and Asaia was consistent with 16S rRNA sequencing, suggesting that population level field screening of the bacterial microbiota may be feasibly integrated into wider resistance monitoring if reliable and reproducible markers associated with phenotype can be identified.

scholarly journals Microbial Community Shift and Role of Bacteria in Rapid Granulation By Using Diatomite

2022 ◽  
Author(s):  
Hazlami Fikri Basri ◽  
Aznah Nor Anuar ◽  
Mohd Hakim Abdul Halim
Keyword(s):  
Microbial Community ◽  
Alpha Diversity ◽  
Granular Sludge ◽  
Community Analysis ◽  
Shannon Index ◽  
Microbial Community Analysis ◽  
Aerobic Granular Sludge ◽  
Granulation Process ◽  
Community Shift ◽  
Seed Sludge

Abstract Aerobic granular sludge (AGS) technology is a promising biological method for modern wastewater treatment. However, granulation time have become a major issue for the application of AGS technology especially in low strength wastewater. Recent studies on granulation are focusing towards rapid start-up granulation process. Diatomite, a friable light-coloured sedimentary rock was introduces in this study to enhanced the granules formation. This study highlight the effect of diatomite towards the microbial community during the transformation of seed sludge until development of granules. DNA extraction and Metagenomic analysis was conducted with three samples (seed sludge, control AGS, AGS diatomite) to compare the microbial community. The microbial community analysis revealed the alpha diversity, phylum and class level, and the abundance of EPS producing bacteria of each bacteria samples respectively. Diatomite has a significant influence towards the microbial diversity (High Shannon index alpha diversity). Also, diatomite promotes the abundance of functional bacteria especially EPS producing bacteria, which seen as a crucial elements in granulation process.

scholarly journals A Pilot Study on the Microbiome of Amblyomma hebraeum Tick Stages Infected and Non-Infected with Rickettsia africae

Pathogens ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 941
Author(s):  
Dalicia Kisten ◽  
Jory Brinkerhoff ◽  
Selaelo Ivy Tshilwane ◽  
Samson Mukaratirwa
Keyword(s):  
Microbial Community ◽  
Pilot Study ◽  
Microbial Community Composition ◽  
Blood Feeding ◽  
Rrna Gene ◽  
Eastern Cape ◽  
Amblyomma Hebraeum ◽  
Rickettsia Africae ◽  
Significant Difference ◽  
Single Genus

Variation in tick microbiota may affect pathogen acquisition and transmission but for many vector species, including Amblyomma hebraeum, components and determinants of the microbiome are unidentified. This pilot study aimed to determine baseline microbial community within A. hebraeum nymphs infected- and non-infected with Rickettsia africae from the environment, and within adult ticks infected- and non-infected with R. africae collected from cattle sampled from two locations in the Eastern Cape province of South Africa. Adult A. hebraeum ticks (N = 13) and A. hebraeum nymph (N = 15) preliminary screened for R. africae were randomly selected and subjected to Illumina sequencing targeting the v3–v4 hypervariable regions of the 16S rRNA gene. No significant difference in microbial community composition, as well as rarefied OTU richness and diversity were detected between adults and nymphs. Nymphs showed a higher richness of bacterial taxa indicating blood-feeding could have resulted in loss of microbial diversity during the moulting stage from nymph to adult. Core OTUs that were in at least 50% of nymphs and adults negative and positive for Rickettsia at 1% minimum relative abundance were Rickettsia, Coxiella and Ruminococcaceae UCG-005 with a single genus Arsenophonus occurring only in nymphs negative for Rickettsia. Ehrlichia spp. was present in only four nymphal ticks positive for Rickettsia. Interestingly, Rickettsia aeschlimannii was found in one nymph and one adult, indicating the first ever detection of the species in A. hebraeum. Furthermore, A. hebraeum harboured a Coxiella-like endosymbiont, which should be investigated further as Coxiella may affect the viability and transmission of other organisms.

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