scholarly journals Uncovering microbial populations in the lumen of neonatal enteral feeding tubes utilising 16s rRNA sequencing

2020 ◽  
Author(s):  
Christopher J Winnard ◽  
Sue Green ◽  
Alison Baylay ◽  
Mark J Johnson ◽  
Mandy Fader ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Variable Region ◽  
Milk Formula ◽  
Feeding Tubes ◽  
Enterococcus Spp ◽  
Rrna Sequencing ◽  
Infant Gut Microbiome ◽  
Limited Culture ◽  
Specific Care ◽  
Care Regimes

AbstractGastrointestinal microbiome is increasingly implicated in the morbidity associated with being born preterm. Enteral tubes (ET) are essential for the nutritional care of preterm infants. Limited culture-based studies have suggested they are colonised by high densities of microorganisms. Microbial DNA was extracted from 60 ETs retrieved from infants in a tertiary neonatal unit and analysed by16s rRNA sequencing of the V4 variable region. Relative abundance analysis on dominant microorganisms demonstrated that compared to breast milk, formula significantly increased abundance of Streptococcus spp and significantly decreased Enterococcus spp and Enterobacteriaceae Vaginal birth was also associated with significantly increased relative abundance of Streptococcus. This study more accurately demonstrates the extent of microbial diversity in neonatal ETs, with feeding regime significantly influencing colonisation patterns. Colonisation with unwanted organisms, as a result of specific care regimes, could result in disruption of the fragile infant gut microbiome, with implications for long-term morbidity.

scholarly journals P851 Effects of conservation time on the diversity and relative abundance of intestinal microbiome in samples of faecal matters

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S655-S655
Author(s):  
M León F ◽  
C A Nieto ◽  
Z Corredor ◽  
C Flórez-Sarmiento ◽  
V Parra-Izquierdo ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Relative Abundance ◽  
High Reliability ◽  
Genetic Material ◽  
Variable Region ◽  
Important Variable ◽  
Intestinal Microbiome ◽  
Three Samples ◽  
Stool Samples ◽  
Changes Over Time

Abstract Background Given the complexity and diversity of the intestinal microbiome, there is a technical challenge of finding the best way to study the factors that affect the quality of the sample to obtain results in a precise an complete way. Objective To establish the effect of storage time under constant cryopreservation conditions (−20°C) in stool samples for the study of the gastrointestinal microbiome Methods A sample of stool was distributed in 3 fractions (1, 2 and 3). Time 0 without cryopreservation and immediate DNA extraction (1). The samples of 15 (2) and 30 (3) days were cryopreserved at −20°C before the extraction of the genetic material. After ultracentrifugation at 4 degrees Celsius, the precipitate was subjected to enzymatic and mechanical lysis to obtain the total DNA. The DNA quality was evaluated techniques to ensure the quality and concentration of genetic material. Once the DNA of the three samples was obtained, they were subjected to the latest generation of a variable region of the 16S gene, using MiSeq technology (Illuminates). Data in relative abundances and frequencies were recorded. Project supported by the Administrative Department of Science, Technology and Innovation-Colciencias Health Call 2017, Code 130877757442 Results About 140 thousand readings were obtained for samples 1 (day 0) and 2 (day 15) and 160 thousand for sample 3 (day 30), with a reading quality Q20% between 97 and 98 and Q30% around 94, indicating a high-reliability value for each of the samples. Regarding the classification from the Operating Taxonomic Unit (OTU), 119, 99 and 106 were reported for samples 1, 2 and 3, respectively. The data obtained revealed changes over time at the level of the main edges reported for normal microbiome (Bacteroidetes, Firmicutes, Actinobacteria) between 1 and 2 vs. sample 3. For Firmicutes and Actinobacteria, decreases in abundance of 34% were observed (samples 1 and 2) at 20% for Firmicutes in sample 3 and from 4% (samples 1 and 2) to 0.8% (sample 3) for Actinobacteria. On the contrary, Bacteroidetes presented an increase in its abundance from 58% (Samples 1 and 2) to 76% (sample 3). The Proteobacterium edge did not show significant changes in its abundance Conclusion It was possible to demonstrate that the cryopreservation time before DNA extraction is an important variable that influences the percentage and integrity of the microbiota from faecal matter. Confirming that the maximum reliable shelf life at −20° in stool samples is up to 15 days, suggesting that for longer storage the temperature decrease up to −80° should be taken into account to maintain stability in the results of relative abundance and bacterial diversity

scholarly journals Characterizing the Composition of the Pediatric Gut Microbiome: A Systematic Review

Nutrients ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 16 ◽  
Author(s):  
Kane E. Deering ◽  
Amanda Devine ◽  
Therese A. O’Sullivan ◽  
Johnny Lo ◽  
Mary C. Boyce ◽  
...  
Keyword(s):  
Systematic Review ◽  
16S Rrna ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Geographical Location ◽  
Short Chain Fatty Acids ◽  
16S Rrna Sequencing ◽  
Short Chain ◽  
Α Diversity ◽  
Rrna Sequencing

The consortium of trillions of microorganisms that live inside the human gut are integral to health. Little has been done to collate and characterize the microbiome of children. A systematic review was undertaken to address this gap (PROSPERO ID: CRD42018109599). MEDLINE and EMBASE were searched using the keywords: “healthy preadolescent children” and “gut microbiome” to 31 August 2018. Of the 815 journal articles, 42 met the inclusion criteria. The primary outcome was the relative abundance of bacteria at the phylum, family, and genus taxonomic ranks. α-diversity, short chain fatty acid concentrations, diet, 16S rRNA sequencing region, and geographical location were documented. The preadolescent gut microbiome is dominated at the phylum level by Firmicutes (weighted overall average relative abundance = 51.1%) and Bacteroidetes (36.0%); genus level by Bacteroides (16.0%), Prevotella (8.69%), Faecalibacterium (7.51%), and Bifidobacterium (5.47%). Geographic location and 16S rRNA sequencing region were independently associated with microbial proportions. There was limited consensus between studies that reported α-diversity and short chain fatty acids. Broadly speaking, participants from non-Western locations, who were less likely to follow a Westernized dietary pattern, had higher α-diversity and SCFA concentrations. Confirmatory studies will increase the understanding of the composition and functional capacity of the preadolescent gut microbiome.

scholarly journals The Role of Enterococcus faecium as a Key Producer and Fermentation Condition as an Influencing Factor in Tyramine Accumulation in Cheonggukjang

Foods ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 915 ◽  
Author(s):  
Young Kyoung Park ◽  
Young Hun Jin ◽  
Jun-Hee Lee ◽  
Bo Young Byun ◽  
Junsu Lee ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Influencing Factor ◽  
Contributing Factors ◽  
Fermentation Temperature ◽  
Soybean Paste ◽  
Safety Risks ◽  
Enterococcus Spp ◽  
Rrna Sequencing ◽  
High Concentrations

The study evaluated the role of Enterococcus faecium in tyramine production and its response to fermentation temperature in a traditional Korean fermented soybean paste, Cheonggukjang. Tyramine content was detected in retail Cheonggukjang products at high concentrations exceeding the recommended limit up to a factor of 14. All retail Cheonggukjang products contained Enterococcus spp. at concentrations of at least 6 Log CFU/g. Upon isolation of Enterococcus strains, approximately 93% (157 strains) produced tyramine at over 100 µg/mL. The strains that produced the highest concentrations of tyramine (301.14–315.29 μg/mL) were identified as E. faecium through 16S rRNA sequencing. The results indicate that E. faecium is one of the major contributing factors to high tyramine content in Cheonggukjang. During fermentation, tyramine content in Cheonggukjang groups co-inoculated with E. faecium strains was highest at 45 °C, followed by 37 °C and 25 °C. The tyramine content of most Cheonggukjang groups continually increased as fermentation progressed, except groups fermented at 25 °C. At 45 °C, the tyramine content occasionally exceeded the recommended limit within 3 days of fermentation. The results suggest that lowering fermentation temperature and shortening duration may reduce the tyramine content of Cheonggukjang, thereby reducing the safety risks that may arise when consuming food with high tyramine concentrations.

scholarly journals Characterization of the gut microbiota in hemodialysis patients with sarcopenia

2021 ◽  
Author(s):  
Qifan Zhou ◽  
Hailin Zhang ◽  
Lixia Yin ◽  
Guilian Li ◽  
Wenxue Liang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Structural Difference ◽  
Hemodialysis Patients ◽  
Maintenance Hemodialysis ◽  
Sequencing Technology ◽  
Β Diversity ◽  
Rrna Sequencing ◽  
Age And Sex

Abstract Purpose Maintenance hemodialysis (MHD) patients are at high risk of sarcopenia. Gut microbiota affects host metabolic and may act in the occurrence of sarcopenia importantly. This study aimed to study the characterization of the gut microbiota in MHD patients with sarcopenia, and to further reveal the complex pathophysiology of sarcopenia in MHD patients. Methods Fecal samples and clinical data were collected from 30 MHD patients with sarcopenia, and 30 age-and-sex-matched MHD patients without sarcopenia in 1 general hospital of Jiangsu Province from December 2020 to March 2021. 16S rRNA sequencing technology was used to analyze the genetic sequence of the gut microbiota for evaluation of the diversity, species composition, and differential microbiota of the two groups. Results Compared to MHD patients without sarcopenia, the ACE index of patients with sarcopenia was lower (P = 0.014), and there was a structural difference in the β-diversity between the two groups (P = 0.001). At the genus level, the relative abundance of Tyzzerella_4 in the sarcopenia group was significantly higher than in the non-sarcopenia group (P = 0.039), and the relative abundance of Megamonas (P = 0.004), Coprococcus_2 (P = 0.038), and uncultured_bacterium_f_Muribaculaceae (P = 0.040) decreased significantly. Conclusion The diversity and structure of the gut microbiota of MHD patients with sarcopenia were altered. The occurrence of sarcopenia in MHD patients may be influenced by gut microbiota.

scholarly journals Gut Microbiota and Related Metabolites Were Disturbed in Ulcerative Colitis and Partly Restored After Mesalamine Treatment

2021 ◽  
Vol 11 ◽  
Author(s):  
Liang Dai ◽  
Yingjue Tang ◽  
Wenjun Zhou ◽  
Yanqi Dang ◽  
Qiaoli Sun ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
Roc Curve Analysis ◽  
Mayo Score ◽  
Rrna Sequencing ◽  
Treatment Naïve ◽  
Stool Samples ◽  
Underlying Mechanisms ◽  
Microbiota Diversity

Mesalamine has been well used in the improvement of ulcerative colitis (UC) in clinics, however, the underlying mechanisms were not well illustrated. To explore its efficacy from the perspective of gut microbiota and related metabolites, we employed 16S rRNA sequencing and metabolomics approaches in stool samples across 14 normal healthy controls (NC group), 10 treatment-naïve UC patients (UC group) and 14 UC patients responded to mesalamine treatment (mesalamine group). We noted that the gut microbiota diversity and community composition were remarkably perturbed in UC group and partially restored by mesalamine treatment. The relative abundance of 192 taxa in genus level were significantly changed in UC group, and 168 genera were significantly altered after mesalamine intervention. Meanwhile, a total of 127 metabolites were significantly changed in UC group and 129 metabolites were significantly altered after mesalamine treatment. Importantly, we observed that many candidates including 49 genera (such as Escherichia-shigella, Enterococcus and Butyricicoccus) and 102 metatoblites (such as isoleucine, cholic acid and deoxycholic acid) were reversed by mesalamine. Spearman correlation analysis revealed that most of the candidates were significantly correlated with Mayo score of UC, and the relative abundance of specific genera were significant correlated with the perturbation of metabolites. Pathway analysis demonstrated that genera and metabolites candidates were enriched in many similar molecular pathways such as amino acid metabolism and secondary metabolites biosynthesis. Importantly, ROC curve analysis identified a gut microbiota signature composed of five genera including Escherichia-Shigella, Streptococcus, Megamonas, Prevotella_9 and [Eubacterium] _coprostanoligenes _group which might be used to distinguish UC group from both NC and mesalamine group. In all, our results suggested that mesalamine might exert a beneficial role in UC by modulating gut microbiota signature with correlated metabolites in different pathways, which may provide a basis for developing novel candidate biomarkers and therapeutic targets of UC.

scholarly journals Rapid molecular identification of fecal origin-colonies growing on Enterococcus spp.-specific culture methods

2016 ◽  
Vol 15 (2) ◽  
pp. 239-250
Author(s):  
Andrée F. Maheux ◽  
Sébastien Bouchard ◽  
Ève Bérubé ◽  
Michel G. Bergeron
Keyword(s):  
Water Quality ◽  
Enterococcus Faecalis ◽  
False Positive ◽  
False Positive Rate ◽  
Culture Methods ◽  
Enterococcus Spp ◽  
Rrna Sequencing ◽  
Positive Rate ◽  
Specific Culture ◽  
Type Strains

The mEI, Chromocult® enterococci, and m-Enterococcus culture-based methods used to assess water quality by the detection of Enterococcus spp. were first compared in terms of sensitivity using (1) 41 different type strains of Enterococcus spp. and (2) environmental colonies identified by 16S rRNA sequencing. Then, two specific-rtPCR assays targeting Enterococcus spp. and Enterococcus faecalis/faecium were tested for their ability to confirm the identity of putative enterococcal colonies. The mEI, Chromocult® enterococci, and m-Enterococcus methods detected β-glucosidase activity for 28 (68.3%), 32 (78.0%), and 12 (29.3%) of the 41 reference enterococcal strains tested, respectively. Analysis with environmental colonies showed that mEI and Chromocult® enterococci media had false positive rates of 4.3% and 5.0%, respectively. Finally, the two rtPCR assays showed a specificity of 100%. Only two (2/19) colonies of E. faecium isolated from mEI agar were not detected by the Enterococcus faecium rtPCR assay, for a sensitivity of 89.5%. Our results showed that Chromocult® enterococci medium recovered more E. faecalis/faecium cells than the two other methods. Thus, the use of Chromocult® enterococci combined with the Enterococcus faecalis/faecium rtPCR assay showed the best combination to decrease the high false-positive rate obtained when the entire Enterococcus genus is targeted.

scholarly journals Effects of Ammonia on Gut Microbiota and Growth Performance of Broiler Chickens

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1716
Author(s):  
Hongyu Han ◽  
Ying Zhou ◽  
Qingxiu Liu ◽  
Guangju Wang ◽  
Jinghai Feng ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Growth Performance ◽  
Relative Abundance ◽  
Broiler Chickens ◽  
Intestinal Microflora ◽  
Rrna Sequencing ◽  
Similar Weight ◽  
Cecal Microflora ◽  
Ammonia Exposure

In order to investigate the influence of ammonia on broiler intestinal microflora and growth performance of broiler chickens, 288 21-day-old male Arbor Acres broilers with a similar weight were randomly divided into four groups with different NH3 levels: 0 ppm, 15 ppm, 25 ppm, and 35 ppm. The growth performance of each group was recorded and analyzed. Additionally, 16s rRNA sequencing was performed on the cecal contents of the 0 ppm group and the 35 ppm group broilers. The results showed the following: a decrease in growth performance in broilers was observed after 35 ppm ammonia exposure for 7 days and 25 ppm ammonia exposure for 14 days. At phylum level, the relative abundance of Proteobacteria phylum was increased after 35 ppm ammonia exposure. At genus level, ammonia increased the relative abundance of Escherichia–Shigella and decreased the relative abundance of Butyricicoccus, Parasutterella, Lachnospiraceae_UCG-010, Ruminococcaceae_UCG-013 and Ruminococcaceae_UCG-004. Negative correlation between Escherichia–Shigella and growth performance, and positive correlation between bacteria genera (including Butyricicoccus, Parasutterella, Lachnospiraceae_UCG-010, Ruminococcaceae_UCG-013 and Ruminococcaceae_UCG-004) and growth performance was observed. In conclusion, ammonia exposure caused changes in the structure of cecal microflora, and several species were either positively or negatively correlated with growth performance. These findings will help enhance our understanding of the possible mechanism by which ammonia affect the growth of broilers.

scholarly journals Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Sihan Li ◽  
Youcheng He ◽  
Haiou Zhang ◽  
Rong Zheng ◽  
Ruoying Xu ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Relative Abundance ◽  
Intestinal Flora ◽  
Intestinal Bacteria ◽  
Symbiotic Relationships ◽  
Study Results ◽  
Rrna Sequencing ◽  
Pcr Technology

AbstractIn this study, the self-extracted constipation treatment of traditional Chinese medicine extracts was applied to constipated rats. To explore the mechanism and role of the Chinese medicine for the treatment of constipation, the 16S rRNA sequencing and qRT-PCR technology were used to analyze the intestinal flora. We found that the relative abundance of Firmicutes with constipation was significantly higher accounted for 86.7%, while the gut microbiota was significantly changed after taking a certain dose of Chinese medicine, greatly increased the relative abundance of Lactobacillus accounted for 23.1%, enhanced the symbiotic relationships of Lactobacillus with other intestinal flora. The total copies of intestinal bacteria in the constipated rats decreased after taking the traditional Chinese medicine. Finally, this study results provides a theoretical basis for the treatment and understand the mechanism and effect of traditional Chinese medicine on rate constipation.

scholarly journals Effect of Oregano Oil and Cobalt Lactate on Sheep In Vitro Digestibility, Fermentation Characteristics and Rumen Microbial Community

Animals ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 118
Author(s):  
Zhengwen Wang ◽  
Xiongxiong Li ◽  
Lingyun Zhang ◽  
Jianping Wu ◽  
Shengguo Zhao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Relative Abundance ◽  
Rumen Fermentation ◽  
Gas Production ◽  
16S Rrna Sequencing ◽  
Molar Ratio ◽  
Fiber Digestibility ◽  
Rrna Sequencing ◽  
Fermentation Parameters

The objective of this experiment was to evaluate the effect of different EOC (0.1425% cobalt lactate + 1.13% oregano essential oil + 98.7275% carrier) levels on in vitro rumen fermentation and microbial changes. Six EOC levels (treatments: 0 mg·L−1, CON; 50 mg·L−1, EOC1; 100 mg·L−1, EOC2; 400 mg·L−1, EOC3; 800 mg·L−1, EOC4 and 1500 mg·L−1, EOC5) were selected to be used to in vitro incubation. The in vitro dry matter digestibility (IVDMD), in vitro neutral detergent fiber digestibility (IVNDFD), in vitro acid detergent fiber digestibility (IVNDFD), pH, ammonia-nitrogen (NH3-N) concentration, total volatile fatty acid (TVFA) concentration and microbial protein (MCP) concentration were measured after 48 h incubation, after which the groups with significant nutrient digestibility and fermentation parameters were subjected to 16S rRNA sequencing. The results showed that the total gas production (GP) of the EOC5 group was higher than that of the other groups after 12 h of in vitro incubation. TVFA, NH3-N and MCP concentrations were also shown to be higher in group EOC5 than those in other groups (p < 0.05), while NH3-N and MCP concentrations in the EOC2 group were lower than those in other groups significantly (p < 0.05). The molar ratio of acetic acid decreased while the molar ratio of propionic acid increased after the addition of EOC. 16S rRNA sequencing revealed that the rumen microbiota was altered in response to adding EOC, especially for the EOC5 treatment, with firmicutes shown to be the most abundant (43.1%). The relative abundance of Rikenellaceae_RC9_gut_group was significantly lower, while the relative abundance of uncultured_bacterium_f_Muribaculaceae and Succiniclasticum was significantly higher in the EOC5 group than those in other groups (p < 0.05). Comprehensive analysis showed that EOC (1500 mg·L−1) could significantly increase gas production, alter sheep rumen fermentation parameters and microbiota composition.

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