Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human

Gupta, Vinod Kumar; Chaudhari, Narendrakumar M.; Iskepalli, Suchismitha; Dutta, Chitra

doi:10.1186/s12864-015-1350-6

Cited by 51 publications

(46 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…indicating high genomic diversity of the different species 140 as well as a high differentiation among 513 strains of the same species, as for instance P. copri 141 . It is well documented that bacteria can 514 modulate the lymphocyte differentiation by the SCFAs (as previously 142 ), whose composition can 515 vary (qualitatively and quantitatively) based on the inflammatory status, as we have recently shown 516 for different intestinal gastrointestinal pathologies, such as celiac disease, adenomatous polyposis and 517 CRC 143 .…”

Section: Statistical Analysis Of the Association Between Tissue Micromentioning

confidence: 99%

Significant and conflicting correlation of IL-9 withPrevotellaandBacteroidesin human colorectal cancer

Niccolai

Russo

Baldi

et al. 2020

Preprint

View full text Add to dashboard Cite

20Background: Colorectal cancer (CRC) is a widespread disease that represents an example of chronic 21 inflammation-associated tumor. In fact, the immune system, besides protecting the host from 22Aim: The cellular and molecular characterization of the immune response and the evaluation of GM 33 composition in healthy and tumor mucosa, focusing on the correlation between cytokines' profile and 34 GM signature. 35 36 Methods: We collected tumoral (CRC) and healthy (CRC-S) mucosa samples of 45 CRC patients. 37 For each sample, we characterized the Tissue Infiltrating Lymphocytes (TIL)'s subset profile and the 38 GM composition. In addition, in 14 CRC patients, we evaluated the CRC and CRC-S molecular 39 inflammatory response (26 cytokines/chemokines) and we correlated this profile with GM 40 composition using the Dirichlet Multinomial Regression. 41 42Results: The analysis of T cells subsets distribution showed that CRC samples displayed higher 43 percentages of Th17, Th2, Tregs, Tc17, Tc1/Tc17, and Tcreg, compared to CRC-S. Notably, also the 44 number of Th9 was higher, even if not significantly, in CRC tissue compared to healthy one. In 45 addition, we found that MIP-1α, IL-1β, IL-2, IP-10, IL-6, IL-8, IL-17A, IFN-γ, TNF-α, MCP-1, IL-46 1α, P-selectin and IL-9 were significantly increased in CRC compared to CRC-S. Moreover, the GM 47 analysis revealed that CRC samples had significantly higher levels of Fusobacteria, Proteobacteria, 48Fusobacterium, Ruminococcus2 (Lachnospiraceae family) and Ruminococcus (Ruminococcaceae 49 family) than CRC-S. Finally, we found that the abundance of Prevotella spp in CRC samples was 50 negatively correlated with IL-17A and positively with IL-9. In addition, the abundance of Bacteroides 51and Escherichia/Shigella species in CRC samples showed a negative association with IL-9 and IP-10 52 respectively. 53 54 Conclusions: Our data show a clear dissimilarity of inflammatory profile and GM composition 55 between the tumor and the adjacent healthy tissue, displaying the generation of a peculiar CRC 56 microenvironment. Interestingly, relating the tissue cytokine profile with the GM composition, we 57 confirmed the presence of a bidirectional crosstalk between the immune response and the host's 58 commensal microorganisms; in detail, we documented for the first time that Prevotella spp. and 59 Bacteroides spp. are correlated (positively and negatively, respectively) with the IL-9, whose role in 60 CRC development is still debated. 61 62 63

show abstract

Section: Statistical Analysis Of the Association Between Tissue Micromentioning

confidence: 99%

Significant and conflicting correlation of IL-9 withPrevotellaandBacteroidesin human colorectal cancer

Niccolai

Russo

Baldi

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Completed bacterial genomes included two for Prevotella copri in samples P2-A and P2-B. This organism lacks a closed reference, in spite of extensive efforts to assemble P. copri and other members of the genus Prevotella 10 . Our previous efforts using read clouds, short reads and synthetic long reads to assemble these communities also had limited success with this organism, never exceeding a genome N50 of 130 kbp, in spite of coverage depth in excess of 4,800x 9 .…”

Section: Main Textmentioning

confidence: 99%

“…In conclusion, our approach assembles the first complete genome of Prevotella copri, an organism with high prevalence in non-western guts and with emerging, potentially strain-specific links to human health and disease 11,12 . The high copy number of IS66 and IS1380 family insertion sequences in this genome limit the effectiveness of short read approaches, despite receiving over 4,800x coverage in an earlier metagenomic sequencing study 9 and extensive isolate sequencing in a separate effort 10 . IS1380 has been previously reported to carry an outward-facing promoter capable of upregulating adjacent gene sequences, and has been found to impact antibiotic resistance gene regulation and resistance phenotype 13 .…”

Section: Main Textmentioning

confidence: 99%

Generating closed bacterial genomes from long-read nanopore sequencing of microbiomes

Bhatt

2018

Preprint

View full text Add to dashboard Cite

7We present the first method for efficient recovery of complete, closed genomes directly 8 from microbiomes using nanopore long-read sequencing and assembly. We apply our approach 9 to three healthy human gut communities and compare results to short read and read cloud 10 approaches. We obtain nine finished genomes including the first reported closed genome of 11Prevotella copri, an organism with highly repetitive genome structure prevalent in non-western 12 human gut microbiomes. longstanding goal of microbiome research. Although current reference-based methods are able 16 to detect known organisms and genes in metagenomes, only de novo approaches are able to 17 characterize novel genome sequences, or accurately place mobile or transferred elements in 18 new genomic contexts. The tremendous diversity and plasticity of bacterial genomes, as well as 19 the difficulty of bacterial isolation and culture, demand effective culture-free methods for 20 producing genomes directly from metagenomes. 21 Current metagenomic sequencing and assembly methods do not typically yield finished 22 bacterial genomes, although previous efforts have achieved single closed genomes in simple 23 communities 1 , or multiple genomes with skilled manual assembly and scaffolding 2 . 24Consequently, genome drafts are formed by grouping (i.e. binning) similar contigs within 25 fragmentary assemblies 3,4 . This is an imperfect process, often compromising the purity or the 26 completeness of the genome reconstruction. As assembly contiguity increases, the sensitivity 27 and specificity of genome binning are improved as fewer, larger contigs need to be grouped to 28 form each genome. Indeed, at the point when genomes are assembled in single contigs, binning 29 becomes unnecessary. Nanopore long read assembly has yielded complete genomes in 30 cultured bacterial isolates 5-8 , suggesting potential for effective assembly in more complex 31 microbial communities. However, the performance of nanopore and other long read approaches 32 in metagenomic sequencing and assembly has been limited by the lack of effective and efficient 33 methods to maximize molecular weight, mass yield and purity of DNA extracted from these 34 samples. 35We present a workflow consisting of stool DNA extraction, nanopore sequencing, 36 assembly and post-processing steps capable of producing multiple complete, circular bacterial 37 genomes directly from metagenomes. Our extraction approach produces microgram quantities 38 of pure, high molecular weight (HMW) DNA suitable for long read sequencing from as little as 39 300 milligrams (mg) of stool. Our computational workflow, consisting of assembly and post-40 processing, does not involve manual intervention in assembly, scaffolding, bacterial isolation, or 41 existing reference coverage of the target metagenome. Thus, this workflow is the first to provide 42 a rapid, simple, cost-effective, automated approach to close high numbers of bacterial genomes 43 directly from metagenomic samples. 44 Short read and read cloud data and ass...

show abstract

“…Our thousands of different microbial species each have their own ecological niche, role, and range of contributions to the whole organism (Gupta et al 2015;Kopac and Klassen 2016;Perez Perez et al 2016). These need to be captured in both safety evaluation and risk assessment.…”

Section: The Human Superorganismmentioning

confidence: 99%

Safety and risk assessment for the human superorganism

Dietert

2017

Human and Ecological Risk Assessment: An International Journal

View full text Add to dashboard Cite

This editorial on safety evaluation and risk assessment for the human superorganism introduces a series of papers arguing for a fundamental shift in how we approach human health risk assessment. In this series emphasis is placed on the risk of infectious disease. Our 21 st st century understanding of human biology is that, as holobionts, we possess a majority of microbial cells and genes. In fact, our microbes fundamentally affect our interactions with the external environment, metabolism, physiology, and risk of both pathology and disease. As holobionts, we require our microbial partners for us to be both complete and healthy. Using the 20 th century understanding of human biology, we failed to capture the effects of the microbiome in evaluating health risks. But 21 st century risk assessments such as those associated with exposure to specific microbial pathogens need to include the human microbiome. Microbiome status will be central in determining the health risks for both individuals and populations.

show abstract

Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human

Cited by 51 publications

References 42 publications

Significant and conflicting correlation of IL-9 withPrevotellaandBacteroidesin human colorectal cancer

Significant and conflicting correlation of IL-9 withPrevotellaandBacteroidesin human colorectal cancer

Generating closed bacterial genomes from long-read nanopore sequencing of microbiomes

Safety and risk assessment for the human superorganism

Contact Info

Product

Resources

About