scholarly journals Emerging Roles of Gut Virome in Pediatric Diseases

2021 ◽  
Vol 22 (8) ◽  
pp. 4127
Author(s):  
Valerio Fulci ◽  
Laura Stronati ◽  
Salvatore Cucchiara ◽  
Ilaria Laudadio ◽  
Claudia Carissimi
Keyword(s):  
Metagenomic Data ◽  
Viral Population ◽  
Human Gut ◽  
Widespread Application ◽  
Shotgun Metagenomics ◽  
Pediatric Diseases ◽  
Inflammatory Bowel ◽  
Systematic Collection

In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial “dark matter” of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.

scholarly journals Discovery, diversity and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts

2021 ◽  
Author(s):  
Anastasia Gulyaeva ◽  
Sanzhima Garmaeva ◽  
Renate A.A.A. Ruigrok ◽  
Daoming Wang ◽  
Niels P. Riksen ◽  
...  
Keyword(s):  
Human Population ◽  
Functional Role ◽  
Novel Species ◽  
Temporal Stability ◽  
Species Level ◽  
Metagenomic Data ◽  
Human Gut ◽  
Genomic Features ◽  
Gut Analysis ◽  
Inflammatory Bowel

The crAss-like phages are a diverse group of related viruses that includes one of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyzed gut metagenomic data collected from more than 2000 individuals from the Netherlands. We discovered 125 novel species-level and 32 novel genus-level clusters of crAss-like phages, all belonging to five previously recognized groups associated with the human gut. Analysis of their genomic features revealed that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts pointed primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explored the temporal stability of crAss-like phages over a 4-year period and identified associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.

scholarly journals Ultrafast and accurate 16S microbial community analysis using Kraken 2

2020 ◽  
Author(s):  
Jennifer Lu ◽  
Steven L Salzberg
Keyword(s):  
16S Rrna ◽  
Ribosomal Rna ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Metagenomic Data ◽  
Human Gut ◽  
Shotgun Metagenomics ◽  
Primary Means ◽  
Unknown Composition

AbstractFor decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely-used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive method. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems. Here we show that, using the same simulated 16S rRNA metagenomic data as previous studies, Kraken 2 and Bracken are up to 300 times faster and also more accurate at 16S profiling than QIIME 2.

scholarly journals Isolation, Detection, and Characterization of Enterotoxigenic Bacteroides fragilis in Clinical Samples

2016 ◽  
Vol 10 (1) ◽  
pp. 57-63 ◽  
Author(s):  
Payam Fathi ◽  
Shaoguang Wu
Keyword(s):  
Bacteroides Fragilis ◽  
Opportunistic Pathogen ◽  
Clinical Samples ◽  
Normal Flora ◽  
Human Gut ◽  
Wide Range ◽  
Inflammatory Bowel ◽  
Generation Sequencing ◽  
Isolated Species

Bacteroides fragilisis an extensively studied anaerobic bacterium comprising the normal flora of the human gut.B. fragilisis known to be one of the most commonly isolated species from clinical samples and has been shown to cause a wide range of pathologies in humans [1, 2]. As an opportunistic pathogenB. fragiliscan cause abscess formation and bacteremia [2]. Additionally in its enterotoxigenic form,B. fragilisis a known cause of diarrheal illness, is associated with inflammatory bowel disease, and has been recently characterized in patients with colon cancer [3 - 5]. As research in the field of the gut microbiome continues to expand at an ever increasing rate due to advances in the availability of next generation sequencing and analysis tools it is important to outline various molecular methods that can be employed in quickly detecting and isolating relevant strains ofB. fragilis. This review outlines methods that are routinely employed in the isolation and detection ofB. fragilis, with an emphasis on characterizing enterotoxigenicB. fragilis(ETBF) strains.

scholarly journals Dynamics of gut microbiome - mediated bile acid metabolism in progression to islet autoimmunity

2021 ◽  
Author(s):  
Santosh Lamichhane ◽  
Partho Sen ◽  
Alex M. Dickens ◽  
Marina Amaral Alves ◽  
Taina Karkonen ◽  
...  
Keyword(s):  
Bile Acid ◽  
Gut Microbiome ◽  
Islet Autoimmunity ◽  
Bile Acid Metabolism ◽  
Islet Autoantibody ◽  
Human Gut ◽  
Shotgun Metagenomics ◽  
Clinical Onset

Previous studies suggest that the human gut microbiome is dysregulated in islet autoimmunity, preceding the clinical onset of type 1 diabetes (T1D). The microbiota of the gut plays an important role in the regulation of bile acid (BA) metabolism. However, not much is known about the regulation of BAs during progression to T1D. Here, we analyzed BAs in a longitudinal series of serum (n= 333) and stool (n= 304) samples, collected at 3, 6, 12, 18, 24 and 36 months of age, from children who developed a single islet autoantibody (P1Ab), multiple islet autoantibodies (P2Ab), and controls (CTRs) who remained autoantibody (AAb) negative during the follow-up. In addition, we analyzed the stool microbiome by shotgun metagenomics in a subgroup of these children (n=111). Factor analysis showed that age had the strongest impact on BA and microbiome profiles. We found that, at an early age, the systemic BA (including taurine and glycine conjugates) and microbial secondary BA pathways were altered in the P2Ab group as compared to the P1Ab or CTR groups. Our findings thus suggest that dysregulated BA metabolism in early life may contribute to the risk and pathogenesis of T1D.

scholarly journals The Endocannabinoid System in Pediatric Inflammatory and Immune Diseases

2019 ◽  
Vol 20 (23) ◽  
pp. 5875 ◽  
Author(s):  
Maura Argenziano ◽  
Chiara Tortora ◽  
Giulia Bellini ◽  
Alessandra Di Paola ◽  
Francesca Punzo ◽  
...  
Keyword(s):  
Social Impact ◽  
Cannabinoid Receptors ◽  
Immune Cell ◽  
Endocannabinoid System ◽  
Pediatric Diseases ◽  
Inflammatory Processes ◽  
Inflammatory Bowel

Endocannabinoid system consists of cannabinoid type 1 (CB1) and cannabinoid type 2 (CB2) receptors, their endogenous ligands, and the enzymes responsible for their synthesis and degradation. CB2, to a great extent, and CB1, to a lesser extent, are involved in regulating the immune response. They also regulate the inflammatory processes by inhibiting pro-inflammatory mediator release and immune cell proliferation. This review provides an overview on the role of the endocannabinoid system with a major focus on cannabinoid receptors in the pathogenesis and onset of inflammatory and autoimmune pediatric diseases, such as immune thrombocytopenia, juvenile idiopathic arthritis, inflammatory bowel disease, celiac disease, obesity, neuroinflammatory diseases, and type 1 diabetes mellitus. These disorders have a high social impact and represent a burden for the healthcare system, hence the importance of individuating more innovative and effective treatments. The endocannabinoid system could address this need, representing a possible new diagnostic marker and therapeutic target.

scholarly journals Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 656 ◽  
Author(s):  
Tasha M. Santiago-Rodriguez ◽  
Emily B. Hollister
Keyword(s):  
High Throughput Sequencing ◽  
Human Microbiome ◽  
Endogenous Retroviruses ◽  
Present Review ◽  
Therapeutic Approaches ◽  
Human Gut ◽  
Bioinformatic Tools ◽  
Immunodeficiency Virus ◽  
Inflammatory Bowel

The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.

scholarly journals Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Ana Martínez-del Campo ◽  
Smaranda Bodea ◽  
Hilary A. Hamer ◽  
Jonathan A. Marks ◽  
Henry J. Haiser ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gene Cluster ◽  
Gut Bacteria ◽  
Functional Gene ◽  
Metagenomic Data ◽  
Human Gut ◽  
Bacterial Gene ◽  
Human Gut Microbiota ◽  
Choline Metabolism

ABSTRACTElucidation of the molecular mechanisms underlying the human gut microbiota's effects on health and disease has been complicated by difficulties in linking metabolic functions associated with the gut community as a whole to individual microorganisms and activities. Anaerobic microbial choline metabolism, a disease-associated metabolic pathway, exemplifies this challenge, as the specific human gut microorganisms responsible for this transformation have not yet been clearly identified. In this study, we established the link between a bacterial gene cluster, the choline utilization (cut) cluster, and anaerobic choline metabolism in human gut isolates by combining transcriptional, biochemical, bioinformatic, and cultivation-based approaches. Quantitative reverse transcription-PCR analysis andin vitrobiochemical characterization of twocutgene products linked the entire cluster to growth on choline and supported a model for this pathway. Analyses of sequenced bacterial genomes revealed that thecutcluster is present in many human gut bacteria, is predictive of choline utilization in sequenced isolates, and is widely but discontinuously distributed across multiple bacterial phyla. Given that bacterial phylogeny is a poor marker for choline utilization, we were prompted to develop a degenerate PCR-based method for detecting the key functional gene choline TMA-lyase (cutC) in genomic and metagenomic DNA. Using this tool, we found that new choline-metabolizing gut isolates universally possessedcutC. We also demonstrated that this gene is widespread in stool metagenomic data sets. Overall, this work represents a crucial step toward understanding anaerobic choline metabolism in the human gut microbiota and underscores the importance of examining this microbial community from a function-oriented perspective.IMPORTANCEAnaerobic choline utilization is a bacterial metabolic activity that occurs in the human gut and is linked to multiple diseases. While bacterial genes responsible for choline fermentation (thecutgene cluster) have been recently identified, there has been no characterization of these genes in human gut isolates and microbial communities. In this work, we use multiple approaches to demonstrate that the pathway encoded by thecutgenes is present and functional in a diverse range of human gut bacteria and is also widespread in stool metagenomes. We also developed a PCR-based strategy to detect a key functional gene (cutC) involved in this pathway and applied it to characterize newly isolated choline-utilizing strains. Both our analyses of thecutgene cluster and this molecular tool will aid efforts to further understand the role of choline metabolism in the human gut microbiota and its link to disease.

Characterization of Helicobacter-induced inflammatory bowel disease in IL-10 -/- and T cell deficient mice

2001 ◽  
Vol 120 (5) ◽  
pp. A523-A523
Author(s):  
A BURICH ◽  
R HERSHBERG ◽  
K WAGGIE ◽  
W ZENG ◽  
J VINEY ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
T Cell ◽  
Bowel Disease ◽  
Inflammatory Bowel ◽  
Deficient Mice

436-P: Characterization of Autoimmunity in the Acceleration of Atherosclerosis in Type 1 Diabetes

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 436-P
Author(s):  
KYOUNGMIN PARK ◽  
QIAN LI ◽  
HYUNSEOK PARK ◽  
RONALD ST-LOUIS ◽  
JIALIN FU ◽  
...  
Keyword(s):  
Type 1 Diabetes
Sign in / Sign up

Export Citation Format

Share Document