scholarly journals Fecal Bacteria as Non-Invasive Biomarkers for Colorectal Adenocarcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Biao Yuan ◽  
Bin Ma ◽  
Jing Yu ◽  
Qingkai Meng ◽  
Tao Du ◽  
...  
Keyword(s):  
Microbial Community ◽  
Early Diagnosis ◽  
Sensitivity And Specificity ◽  
Gut Microbiome ◽  
Colorectal Adenocarcinoma ◽  
Malignant Tumors ◽  
High Sensitivity ◽  
Microbial Community Analysis ◽  
Microbial Composition ◽  
Non Invasive

Colorectal adenocarcinoma (CRC) ranks one of the five most lethal malignant tumors both in China and worldwide. Early diagnosis and treatment of CRC could substantially increase the survival rate. Emerging evidence has revealed the importance of gut microbiome on CRC, thus fecal microbial community could be termed as a potential screen for non-invasive diagnosis. Importantly, few numbers of bacteria genus as non-invasive biomarkers with high sensitivity and specificity causing less cost would be benefitted more in clinical compared with the whole microbial community analysis. Here we analyzed the gut microbiome between CRC patients and healthy people using 16s rRNA sequencing showing the divergence of microbial composition between case and control. Furthermore, ExtraTrees classifier was performed for the classification of CRC gut microbiome and heathy control, and 13 bacteria were screened as biomarkers for CRC. In addition, 13 biomarkers including 12 bacteria genera and FOBT showed an outstanding sensitivity and specificity for discrimination of CRC patients from healthy controls. This method could be used as a non-invasive method for CRC early diagnosis.

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.

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 Efficacy of Monocyte Distribution Width in the Early Diagnosis of Sepsis: A Diagnostic Meta-Analysis

2021 ◽  
Author(s):  
Jiahao Chen ◽  
Qiang Guo
Keyword(s):  
Early Diagnosis ◽  
Large Scale ◽  
Meta Analysis ◽  
Delayed Diagnosis ◽  
Area Under The Curve ◽  
High Sensitivity ◽  
Inexpensive Method ◽  
Diagnostic Efficacy ◽  
Distribution Width ◽  
Non Invasive

Abstract Background: Delayed diagnosis of sepsis urgently requires a fast, convenient, and inexpensive method to improve the early diagnosis of sepsis. Increasing evidence showed that monocyte distribution width (MDW) could be used as a non-invasive biomarker with high sensitivity and specificity for the early diagnosis of sepsis. However, the accuracy and reliability of its diagnosis are still controversial in different studies. Method: A meta-analysis of all available studies regarding the association between MDW and the diagnosis of sepsis was performed to systematically evaluate the diagnostic efficacy of MDW in the prediction of sepsis. Results: The estimated results of all eight studies are as follows: sensitivity, 0.84 (95% CI 0.77, 0.90); specificity, 0.68 (95% CI 0.54, 0.80); PLR, 2.7 (95% CI 1.8, 4.1); NLR, 0.23 (95% CI 0.15, 0.35); DOR is 12 (95% CI 5, 25). The corresponding overall area under the curve is 0.85 (95% CI 0.82, 0.88). Conclusion: In conclusion, this meta-analysis demonstrates that MDW has high accuracy in distinguishing patients with sepsis from healthy controls for early diagnosis of sepsis. However, large-scale prospective studies and joint diagnosis with other indicators are urgently required to confirm our findings and their utilization for routine clinical diagnosis in the future.

scholarly journals Community composition and development of the post-weaning piglet gut microbiome

2020 ◽  
Author(s):  
Daniela Gaio ◽  
Matthew Z DeMaere ◽  
Kay Anantanawat ◽  
Graeme J Eamens ◽  
Michael Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Antibiotic Treatment ◽  
Gut Microbiome ◽  
Treatment Effects ◽  
Sequence Data ◽  
Microbial Community Composition ◽  
Dominant Factor ◽  
Microbial Composition

Abstract BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. Studies have previously investigated the effects of probiotics as alternatives to antibiotic treatment for the prevention of post-weaning diarrhea. In order to describe the post-weaning gut microbiota, and the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we processed over 800 faecal time-series samples from 126 piglets and 42 sows, generating over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework.ResultsFactors such as age, litter effects, and breed, by significantly correlating with gut microbial community shifts, can be major confounding factors in the assessment of treatment effects. Intramuscular antibiotic treatment and probiotic treatments were found to correlate with alpha and beta diversity, as well as with a transient establishment of Mollicutes and Lactobacillales, respectively. We found the abundance of certain taxa to correlate with weight gain.ConclusionsOur findings demonstrate that breed, litter, and age, are important contributors to variation in the community composition, and that treatment effects of the antibiotic and probiotic treatments were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The current study shows, by means of a phylogenetic diversity framework, that the post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.

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 Succession of the Gut Microbiome in the Tibetan Population of Minjiang River Basin

2020 ◽  
Author(s):  
Jun Li ◽  
Lin Sun ◽  
Chunfeng Mo ◽  
Xiangsheng Fu ◽  
Baijun Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Altitude ◽  
River Basin ◽  
Gut Microbiome ◽  
Tibet Plateau ◽  
Gut Microflora ◽  
Microbial Composition ◽  
Tibetan Population ◽  
Minjiang River ◽  
Gut Microbial Community

Abstract Background: Tibetans are one of the oldest ethnic groups in China and South Asia. Tibetan has a unique lifestyle and a long history, which leads to the particularity of their gut microflora in composition and function. Different from the Tibetan population on the Qinghai-Tibet Plateau, Tibetans in Minjiang River Basin have gradually increased their migration to Chengdu Plain in recent years. Based on the analysis of 1059 Tibetans in the Minjiang River Basin at an altitude of 500-4001m, we found that the dominant phylum of Tibetan population is Bacteroidea and Firmicum, and the main genera are Prevotella and Bacteroides. These findings reflect the characteristics of Tibetan population. Results: In order to further study the factors affecting gut microbial composition of Tibetan population, 115 total parameters of 7 categories were evaluated. The results showed that altitude was the most important factor affecting the variation of microbial community in Tibetan population, and the change of altitude promoted the succession of gut microbial community. In the process of migration from high altitude to plain, the intestinal microbial composition of late immigrants was similar to that of plateau aborigines, while that of early immigrants was similar to that of plain aborigines. Migration to Tibet is related to the loss of indigenous gut microbial community species. In addition, from low altitude to high altitude, the similarity of microbial community with high altitude population increased with the reproduction of offspring after marriage. And the change of these flora will affect the metabolism, disease and cell function of Tibetan population. The other two sets (AGP and Z208) of altitude data also show the impact of altitude on the microbial community. Conclusions: This is the first large-scale study on the influencing factors of gut microflora in Tibetan population. Our study confirmed that altitude change is the most important factor affecting the distribution of Tibetan population flora, and provided abundant and unique data to explore the interaction of impact parameter-gut microbiome-host function and disease.

scholarly journals The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 70
Author(s):  
Lore Bulteel ◽  
Shira Houwenhuyse ◽  
Steven A. J. Declerck ◽  
Ellen Decaestecker
Keyword(s):  
Microbial Community ◽  
Daphnia Magna ◽  
Gut Microbiome ◽  
Community Treatment ◽  
Control Treatment ◽  
Transplant Experiment ◽  
Host Genotype ◽  
Microbial Composition ◽  
Gut Microbial Community

Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.

scholarly journals Saliva Exhibits High Sensitivity and Specificity for the Detection of SARS-COV-2

Diseases ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 38
Author(s):  
Ibrahim Warsi ◽  
Zohaib Khurshid ◽  
Hamda Shazam ◽  
Muhammad Farooq Umer ◽  
Eisha Imran ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
High Sensitivity ◽  
Minimal Risk ◽  
Non Invasive ◽  
Oral Fluids ◽  
Home Testing ◽  
Screening Strategies ◽  
Online Calculator ◽  
And Control ◽  
High Degree

In the wake of the COVID-19 pandemic, it is crucial to assess the application of a multitude of effective diagnostic specimens for conducting mass testing, for accurate diagnosis and to formulate strategies for its prevention and control. As one of the most versatile and amenable specimen options, saliva offers great advantages for widespread screening strategies due to its non-invasive properties, cost-effectiveness, excellent stability and minimal risk of cross-infection. This review attempts to outline the scientific rationale for detection of SARS-COV-2 in saliva specimens. By combining the data obtained from ten chosen published clinical studies, we calculated the pooled sensitivity and specificity using an online calculator. Through evidence, we established that SARS-COV-2 is detectable in saliva with a high degree of diagnostic sensitivity (87%) and specificity (98%). We also presented a review of emerging technologies approved by the FDA for detection of SARS-COV-2 in oral fluids (saliva and sputum) using polymerase chain reaction methods. Given the challenges involved in obtaining invasive specimens from the naso- and oropharynx, saliva can serve as an easy to collect diagnostic specimen for screening in the work environment, schools and for home testing. Furthermore, saliva offers the opportunity to screen early cases that can be missed by invasive sampling.

scholarly journals Host Phylogeny Determines The Gut Microbial Landscape of Cephalopods

2021 ◽  
Author(s):  
Woorim Kang ◽  
Pil Soo Kim ◽  
Euon Jung Tak ◽  
Hojun Sung ◽  
Na-Ri Shin ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Circulatory System ◽  
Illumina Miseq ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Host Phylogeny ◽  
Gut Microbial Community

Abstract BackgroundCompared to vertebrate gut microbiomes, little is known about the factors shaping the gut microbiomes in invertebrates, especially in non-insect invertebrates. Class Cephalopoda is the only group in the phylum Mollusca characterized by a closed circulatory system and a well-differentiated digestive system to process their carnivorous diet. Despite their key phylogenetic position for comparative studies as well as their ecological and commercial importances, analyses of the cephalopod gut microbiome are limited. In this study, we characterized the gut microbiota of six species of wild cephalopods by Illumina MiSeq sequencing of 16S rRNA gene amplicons.ResultsEach cephalopod gut consisted of a distinct consortium of microbes. Photobacterium and Mycoplasma were prevalent in all cephalopod hosts and were identified as core taxa. The gut microbial composition reflected host phylogeny. The importance of host phylogeny was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma, although Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Further, we showed that class Cephalopoda has a distinct gut microbial community from those of other molluscan groups. The gut microbiota of the phylum Mollusca was determined by host phylogeny, diet, and environment (aquatic vs. terrestrial).ConclusionWe provide the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of the distinctive microbes and strongly associated with their phylogeny. The genera Photobacterium and Mycoplasma are core taxa in the cephalopod gut microbiota. Collectively, our findings of this study provide evidence that cephalopod and mollusk gut microbiomes reflect phylogeny, environment, and the diet of the host and these data can be suggested to establish future directions for invertebrate gut microbiome research.

scholarly journals A comparison of neutrophil gelatinase-associated lipocalin and immature to total neutrophil ratio for diagnosing early-onset neonatal sepsis

2016 ◽  
Vol 56 (2) ◽  
pp. 107
Author(s):  
Rocky Wilar ◽  
Dasril Daud ◽  
Suryani As’ad ◽  
Dwi Bahagia Febriani ◽  
Mina Mina
Keyword(s):  
Early Diagnosis ◽  
Sensitivity And Specificity ◽  
Neonatal Sepsis ◽  
Early Onset ◽  
High Sensitivity ◽  
Clinical Syndrome ◽  
Cross Sectional ◽  
Predictive Values ◽  
Neutrophil Gelatinase Associated Lipocalin ◽  
Neutrophil Gelatinase

Background Neonatal sepsis is a clinical syndrome caused by the invasion of microorganisms into the bloodstream. Early diagnosis of early-onset neonatal sepsis (EONS) is difficult. Laboratory tests with high sensitivity and specificity are needed in order to make early diagnoses in newborns.Objective To compare the sensitivity and specificity of neutrophil gelatinase-associated lipocalin (NGAL) and immature to total (IT) neutrophil ratio for the diagnosis of early-onset neonatal sepsis.Methods This observational study with cross-sectional design was conducted in the Neonatology Division, Prof. R. D. Kandou General Hospital from November 2012 to April 2014. Consecutive sampling was applied. There were 103 newborns with suspected EONS who fulfilled the inclusion criteria. Complete blood counts, blood cultures, as well as NGAL and IT ratio measurements were performed.Results NGAL was not significantly more sensitive than IT ratio [80.4% vs. 67.3%, respectively; (P=0.058)]. However, NGAL had lower specificity than IT ratio (27.7% vs. 50.0%, respectively; P=0.016). The positive predictive values (57.0% vs. 64.9%, respectively; P=0.176), and negative predictive values (54.2% vs. 52.6%, respectively; P=0.451) were similar in both diagnostic tests.Conclusion Immature to total neutrophil (IT) ratio has higher specificity compared to NGAL for early diagnosis of EONS. However, the difference in sensitivity between the two test is not statistically significant.

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