scholarly journals A Shotgun Metagenomic Sequencing Exploration of Cabernet Sauvignon Grape Must Reveals Yeast Hydrolytic Enzymes

2021 ◽  
Vol 42 (2) ◽  
Author(s):  
S. Ghosh ◽  
B. Divol ◽  
M.E. Setati
Keyword(s):  
Hydrolytic Enzymes ◽  
Cabernet Sauvignon ◽  
Metagenomic Sequencing ◽  
Grape Must ◽  
Shotgun Metagenomic Sequencing

scholarly journals Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

2021 ◽  
Vol 9 (4) ◽  
pp. 707
Author(s):  
J. Christopher Noone ◽  
Fabienne Antunes Ferreira ◽  
Hege Vangstein Aamot
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Virulence Gene ◽  
Orthopaedic Implant ◽  
Metagenomic Sequencing ◽  
Gene Detection ◽  
Shotgun Metagenomic Sequencing ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

scholarly journals Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1041
Author(s):  
Rita Mormando ◽  
Alan J. Wolfe ◽  
Catherine Putonti
Keyword(s):  
Jc Virus ◽  
Sequence Similarity ◽  
Bk Virus ◽  
Data Sets ◽  
Metagenomic Sequencing ◽  
Significant Sequence Similarity ◽  
Sequence Identity ◽  
Shotgun Metagenomic Sequencing ◽  
Urinary Microbiome ◽  
Six Genes

Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity.

scholarly journals Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis

2018 ◽  
Vol 57 (2) ◽  
Author(s):  
Qun Yan ◽  
Yu Mi Wi ◽  
Matthew J. Thoendel ◽  
Yash S. Raval ◽  
Kerryl E. Greenwood-Quaintance ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Antibacterial Resistance ◽  
Sequencing Data ◽  
Bacterial Detection ◽  
Shotgun Metagenomic Sequencing ◽  
Prosthetic Joint ◽  
Validation Set ◽  
Fluid Culture

ABSTRACT We previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach that we used is that data analysis was time-consuming and specialized bioinformatics expertise was required, both of which are barriers to routine clinical use. Fortunately, automated commercial analytic platforms that can interpret shotgun metagenomic data are emerging. In this study, we evaluated the CosmosID bioinformatics platform using shotgun metagenomic sequencing data derived from 408 sonicate fluid samples from our prior study with the goal of evaluating the platform vis-à-vis bacterial detection and antibiotic resistance gene detection for predicting staphylococcal antibacterial susceptibility. Samples were divided into a derivation set and a validation set, each consisting of 204 samples; results from the derivation set were used to establish cutoffs, which were then tested in the validation set for identifying pathogens and predicting staphylococcal antibacterial resistance. Metagenomic analysis detected bacteria in 94.8% (109/115) of sonicate fluid culture-positive PJIs and 37.8% (37/98) of sonicate fluid culture-negative PJIs. Metagenomic analysis showed sensitivities ranging from 65.7 to 85.0% for predicting staphylococcal antibacterial resistance. In conclusion, the CosmosID platform has the potential to provide fast, reliable bacterial detection and identification from metagenomic shotgun sequencing data derived from sonicate fluid for the diagnosis of PJI. Strategies for metagenomic detection of antibiotic resistance genes for predicting staphylococcal antibacterial resistance need further development.

scholarly journals Human gut microbial communities dictate efficacy of anti-PD-1 therapy in a humanized microbiome mouse model of glioma

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Kory J Dees ◽  
Hyunmin Koo ◽  
J Fraser Humphreys ◽  
Joseph A Hakim ◽  
David K Crossman ◽  
...  
Keyword(s):  
Mouse Model ◽  
Microbial Communities ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Healthy Human ◽  
Fecal Transplantation ◽  
Host Interaction ◽  
Shotgun Metagenomic Sequencing ◽  
Mouse Lines

Abstract Background Although immunotherapy works well in glioblastoma (GBM) preclinical mouse models, the therapy has not demonstrated efficacy in humans. To address this anomaly, we developed a novel humanized microbiome (HuM) model to study the response to immunotherapy in a preclinical mouse model of GBM. Methods We used 5 healthy human donors for fecal transplantation of gnotobiotic mice. After the transplanted microbiomes stabilized, the mice were bred to generate 5 independent humanized mouse lines (HuM1-HuM5). Results Analysis of shotgun metagenomic sequencing data from fecal samples revealed a unique microbiome with significant differences in diversity and microbial composition among HuM1-HuM5 lines. All HuM mouse lines were susceptible to GBM transplantation, and exhibited similar median survival ranging from 19 to 26 days. Interestingly, we found that HuM lines responded differently to the immune checkpoint inhibitor anti-PD-1. Specifically, we demonstrate that HuM1, HuM4, and HuM5 mice are nonresponders to anti-PD-1, while HuM2 and HuM3 mice are responsive to anti-PD-1 and displayed significantly increased survival compared to isotype controls. Bray-Curtis cluster analysis of the 5 HuM gut microbial communities revealed that responders HuM2 and HuM3 were closely related, and detailed taxonomic comparison analysis revealed that Bacteroides cellulosilyticus was commonly found in HuM2 and HuM3 with high abundances. Conclusions The results of our study establish the utility of humanized microbiome mice as avatars to delineate features of the host interaction with gut microbial communities needed for effective immunotherapy against GBM.

scholarly journals Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

2020 ◽  
Author(s):  
Caroline Ivanne Le Roy ◽  
Alexander Kurilshikov ◽  
Emily Leeming ◽  
Alessia Visconti ◽  
Ruth Bowyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Visceral Fat ◽  
Gut Microbiome ◽  
Body Weight Gain ◽  
Healthy Eating Index ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

scholarly journals The human microbiome in hematopoiesis and hematologic disorders

Blood ◽  
2015 ◽  
Vol 126 (3) ◽  
pp. 311-318 ◽  
Author(s):  
Veronica E. Manzo ◽  
Ami S. Bhatt
Keyword(s):  
Community Structure ◽  
Human Health ◽  
Ribosomal Rna ◽  
Human Microbiome ◽  
Human Cells ◽  
Metagenomic Sequencing ◽  
Hematologic Disorders ◽  
Hematologic Diseases ◽  
Shotgun Metagenomic Sequencing

AbstractHumans are now understood to be in complex symbiosis with a diverse ecosystem of microbial organisms, including bacteria, viruses, and fungi. Efforts to characterize the role of these microorganisms, commonly referred as the microbiota, in human health have sought to answer the fundamental questions of what organisms are present, how are they functioning to interact with human cells, and by what mechanism are these interactions occurring. In this review, we describe recent efforts to describe the microbiota in healthy and diseased individuals, summarize the role of various molecular technologies (ranging from 16S ribosomal RNA to shotgun metagenomic sequencing) in enumerating the community structure of the microbiota, and explore known interactions between the microbiota and humans, with a focus on the microbiota’s role in hematopoiesis and hematologic diseases.

Abstract P174: Adiposity Mediates the Association Between Gut Microbial Diversity and Hypertension: Cardia Study

Circulation ◽  
2020 ◽  
Vol 141 (Suppl_1) ◽  
Author(s):  
Yuichiro Yano ◽  
Anju Lulla ◽  
Annie Green Howard ◽  
Samuel Gidding ◽  
Paul Muntner ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Antihypertensive Medication ◽  
Diversity Index ◽  
Metagenomic Sequencing ◽  
Mediation Analyses ◽  
Shotgun Metagenomic Sequencing ◽  
Stool Samples ◽  
Microbiota Diversity ◽  
Microbial Effects

Introduction: We have shown that gut microbial diversity is associated with hypertension in the Coronary Artery Risk Development in Young Adults (CARDIA) Study. Animal models have documented gut microbial effects on adiposity, a known risk factor for hypertension. The extent to which adiposity may mediate the association between the gut microbiome and hypertension has not been studied. Hypothesis: We hypothesize that adiposity is a mediator of the association between gut microbial diversity and hypertension. Methods: We analyzed data from the CARDIA Study (480 participants). Shotgun metagenomic sequencing was performed on DNA extracted from stool samples collected at the Year 30 exam (2015-2016). Taxonomic classification of sequenced reads was performed using Kraken2. Within-person gut microbial diversity was assessed at the genus level using the Shannon Diversity Index and richness (number of distinct genera); lower values indicate less diversity. Hypertension was defined as systolic BP ≥140, diastolic BP ≥90 mm Hg, or taking antihypertensive medication. We performed mediation analyses to quantify the percentage of the total estimated effect of gut microbial diversity on hypertension that is mediated by adiposity as assessed using body mass index (BMI). Results: Mean age of the participants was 55.1 (3.4) years, 47% were African American, and 53% were female. In multivariable-adjusted mediation analysis, BMI explained on average 26-34% of the association between gut microbiota diversity and hypertension (Table). Results were robust to adjustment for sociodemographic variables (Model 2) and health behaviors (Model 3). Conclusions: Approximately one-third of the total effect of gut microbial diversity on hypertension is mediated through adiposity.

scholarly journals The gut microbiome in konzo

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Matthew S. Bramble ◽  
Neerja Vashist ◽  
Arthur Ko ◽  
Sambhawa Priya ◽  
Céleste Musasa ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Bacterial Species ◽  
Sub Saharan Africa ◽  
Metagenomic Sequencing ◽  
Childbearing Age ◽  
Shotgun Metagenomic Sequencing ◽  
Republic Of The Congo ◽  
Study Population ◽  
Sub Saharan ◽  
Insight Into

AbstractKonzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.

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