MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics, and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarters of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.

Download Full-text

Phages - bacteria interactions network of the healthy human gut

10.1101/2020.05.13.093716 ◽

2020 ◽

Cited By ~ 1

Author(s):

Martial Marbouty ◽

Agnès Thierry ◽

Romain Koszul

Keyword(s):

Microbial Communities ◽

Single Sample ◽

Large Network ◽

Sample Analysis ◽

Human Gut ◽

Healthy Human ◽

Human Microbiota ◽

Crucial Information ◽

Interactions Network

AbstractWith an estimated 1031 particles on earth, bacteriophages are the most abundant genomic entities across all habitats and important drivers of microbial communities. Growing evidence suggest that they play roles in intestinal human microbiota homeostasis, and recent metagenomics studies on the viral fraction of this ecosystem have provided crucial information about their diversity and specificity. However, the bacterial hosts of this viral fraction, a necessary information to characterize further the balance of these ecosystems, remain poorly characterized. Here we unveil, using an enhanced metagenomic Hi-C approach, a large network of 6,651 host-phage relationships in the healthy human gut allowing to study in situ phage-host ratio. We notably found that half of these contigs appear to be sleeping prophages whereas ¼ exhibit a higher coverage than their associated MAG representing potentially active phages impacting the ecosystem. We also detect different candidate members of the crAss-like phage family as well as their bacterial hosts showing that these elusive phages infect different genus of Bacteroidetes. This work opens the door to single sample analysis and concomitant study of phages and bacteria in complex communities.

Download Full-text

Changes in Human Gut Microbiota Composition Are Linked to the Energy Metabolic Switch During Ten Days of Fasting

SSRN Electronic Journal ◽

10.2139/ssrn.3378696 ◽

2019 ◽

Author(s):

Robin Mesnage ◽

Franziska Grundler ◽

Andreas Schwiertz ◽

Yvon Le Maho ◽

Françoise Wilhelmi de Toledo

Keyword(s):

Gut Microbiota ◽

Microbiota Composition ◽

Human Gut ◽

Metabolic Switch ◽

Human Gut Microbiota ◽

Gut Microbiota Composition

Download Full-text

Sex differences in the phylum‐level human gut microbiota composition

BMC Microbiology ◽

10.1186/s12866-021-02198-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Alexander Koliada ◽

Vladislav Moseiko ◽

Mariana Romanenko ◽

Oleh Lushchak ◽

Nadiia Kryzhanovska ◽

...

Keyword(s):

Sex Differences ◽

Gut Microbiota ◽

Age Groups ◽

Microbiota Composition ◽

Human Gut ◽

Cross Sectional ◽

Total N ◽

Human Gut Microbiota ◽

Gut Microbiota Composition

Abstract Background Evidence was previously provided for sex-related differences in the human gut microbiota composition, and sex-specific discrepancy in hormonal profiles was proposed as a main determinant of these differences. On the basis of these findings, the assumption was made on the role of microbiota in the sexual dimorphism of human diseases. To date, sex differences in fecal microbiota were demonstrated primarily at lower taxonomic levels, whereas phylum-level differences between sexes were reported in few studies only. In the present population-based cross-sectional research, sex differences in the phylum-level human gut microbiota composition were identified in a large (total n = 2301) sample of relatively healthy individuals from Ukraine. Results Relative abundances of Firmicutes and Actinobacteria, as determined by qRT-PCR, were found to be significantly increased, while that of Bacteroidetes was significantly decreased in females compared to males. The Firmicutes to Bacteroidetes (F/B) ratio was significantly increased in females compared to males. Females had 31 % higher odds of having F/B ratio more than 1 than males. This trend was evident in all age groups. The difference between sexes was even more pronounced in the elder individuals (50+): in this age group, female participants had 56 % higher odds of having F/B ratio > 1 than the male ones. Conclusions In conclusion, sex-specific differences in the phylum-level intestinal microbiota composition were observed in the Ukraine population. The F/B ratio was significantly increased in females compared to males. Further investigation is needed to draw strong conclusions regarding the mechanistic basis for sex-specific differences in the gut microbiota composition and regarding the role of these differences in the initiation and progression of human chronic diseases.

Download Full-text

Competition between Metals for Binding to Methanobactin Enables Expression of Soluble Methane Monooxygenase in the Presence of Copper

Applied and Environmental Microbiology ◽

10.1128/aem.03151-14 ◽

2014 ◽

Vol 81 (3) ◽

pp. 1024-1031 ◽

Cited By ~ 16

Author(s):

Bhagyalakshmi Kalidass ◽

Muhammad Farhan Ul-Haque ◽

Bipin S. Baral ◽

Alan A. DiSpirito ◽

Jeremy D. Semrau

Keyword(s):

Methane Monooxygenase ◽

High Specificity ◽

Copper Uptake ◽

Content Type ◽

Soluble Methane Monooxygenase ◽

Sds Page ◽

Genes Encoding ◽

Key Factor ◽

Membrane Bound

ABSTRACTIt is well known that copper is a key factor regulating expression of the two forms of methane monooxygenase found in proteobacterial methanotrophs. Of these forms, the cytoplasmic, or soluble, methane monooxygenase (sMMO) is expressed only at low copper concentrations. The membrane-bound, or particulate, methane monooxygenase (pMMO) is constitutively expressed with respect to copper, and such expression increases with increasing copper. Recent findings have shown that copper uptake is mediated by a modified polypeptide, or chalkophore, termed methanobactin. Although methanobactin has high specificity for copper, it can bind other metals, e.g., gold. Here we show that inMethylosinus trichosporiumOB3b, sMMO is expressed and active in the presence of copper if gold is also simultaneously present. Such expression appears to be due to gold binding to methanobactin produced byM. trichosporiumOB3b, thereby limiting copper uptake. Such expression and activity, however, was significantly reduced if methanobactin preloaded with copper was also added. Further, quantitative reverse transcriptase PCR (RT-qPCR) of transcripts of genes encoding polypeptides of both forms of MMO and SDS-PAGE results indicate that both sMMO and pMMO can be expressed when copper and gold are present, as gold effectively competes with copper for binding to methanobactin. Such findings suggest that under certain geochemical conditions, both forms of MMO may be expressed and activein situ. Finally, these findings also suggest strategies whereby field sites can be manipulated to enhance sMMO expression, i.e., through the addition of a metal that can compete with copper for binding to methanobactin.

Download Full-text

Effects of phlorotannin and polysaccharide fractions of brown seaweed Silvetia compressa on human gut microbiota composition using an in vitro colonic model

Journal of Functional Foods ◽

10.1016/j.jff.2021.104596 ◽

2021 ◽

Vol 84 ◽

pp. 104596

Author(s):

Benjamín Vázquez-Rodríguez ◽

Liliana Santos-Zea ◽

Erick Heredia-Olea ◽

Laura Acevedo-Pacheco ◽

Arlette Santacruz ◽

...

Keyword(s):

Gut Microbiota ◽

Brown Seaweed ◽

Microbiota Composition ◽

Human Gut ◽

Human Gut Microbiota ◽

Gut Microbiota Composition

Download Full-text

Tumor Microenvironment-Triggered In-Situ Cancer Vaccines with Dual Immunogenic Cell Death Inductions for Elevated Antitumor and Antimetastatic Therapy

Nanoscale ◽

10.1039/d1nr02018h ◽

2021 ◽

Author(s):

Jun Lin ◽

Binbin Ding ◽

Pan Zheng ◽

Dong Li ◽

Meifang Wang ◽

...

Keyword(s):

Cell Death ◽

Tumor Microenvironment ◽

Immune Responses ◽

Cancer Immunotherapy ◽

Cancer Vaccines ◽

High Specificity ◽

The Body ◽

Immunogenic Cell Death ◽

Specific Antigens

Cancer vaccine is to make tumor-specific antigens into vaccines, which then are injected back into the body to activate immune responses for cancer immunotherapy. Despite the high specificity and therapeutic...

Download Full-text

Iso-chromosome 12p Analysis by Fluorescent In-Situ Hybridization: An Academic Institutional Experience

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqab191.150 ◽

2021 ◽

Vol 156 (Supplement_1) ◽

pp. S72-S72

Author(s):

P P Patwardhan ◽

S Satturwar ◽

R Dhir ◽

G M Quiroga-Garza

Keyword(s):

In Situ Hybridization ◽

Germ Cell ◽

Fluorescent In Situ Hybridization ◽

Clinical Presentation ◽

Germ Cell Tumors ◽

High Specificity ◽

Testicular Germ Cell ◽

Chromosome 12P ◽

Institutional Experience

Abstract Introduction/Objective Chromosome 12 abnormalities like iso-chromosome 12p (i12p) and amplification of 12p are seen in majority (89%) of the primary and metastatic testicular germ cell tumors (TGCTs). i12p can be detected by karyotyping, fluorescent in-situ hybridization (FISH) or reverse transcriptase polymerase chain reaction. The aim of this study was to review i12p FISH data at our institution and assess the clinical utility. Methods/Case Report Laboratory information system was queried over a period of 15 years to search for cases where i12p FISH test was requested. FISH test was performed using TelVysion 12p telomeric probe and CEP 12 centromere probe on paraffin-embedded tissue or cell blocks. A ratio of 12ptel/CEP12 signal of 1.4 or greater was considered as positive. Patient demographics, clinical presentation, pathologic findings, and follow-up data were documented and correlated. Results (if a Case Study enter NA) Total 58 cases were identified with an age range of 14 to 76 years. Majority were male (M=52, F=6). Of these cases, 15 were testicular and 43 extra-testicular cases that included resection (n=35), biopsy (n=20) and cell-blocks (n=3). i12p was detected in 8 out of 15 testicular cases while i12p was detected in 16 out of the 43 extra-testicular cases. The extra- testicular cases included 17 retroperitoneal lesions, 8 lesions from the mediastinum, 6 lymph nodes from other sites and 12 miscellaneous lesions. Using pathology diagnosis with immunohistochemistry as gold standard, overall sensitivity was 60% and specificity was 86%. There were 3 false positive cases [Benign testicular parenchyma (n=1), suspicious for germ cell neoplasia in-situ (n=1) and undifferentiated epithelioid neoplasm (n=1)]. Conclusion Our results show that although the sensitivity was limited, FISH test for i12p demonstrated high specificity(86%) for diagnosis of primary or metastatic TGCTs. As an adjunct test, i12p FISH can help identify and further characterize a significant number of GCTs with unusual morphology or clinical presentation.

Download Full-text

Baseline human gut microbiota profile in healthy people and standard reporting template

10.1101/445353 ◽

2018 ◽

Author(s):

Charles Hadley King ◽

Hiral Desai ◽

Allison C. Sylvetsky ◽

Jonathan LoTempio ◽

Shant Ayanyan ◽

...

Keyword(s):

Dark Matter ◽

Regulatory Agencies ◽

Fecal Transplant ◽

Human Gut ◽

Healthy Human ◽

Comprehensive Knowledge ◽

Analysis Workflow ◽

Standard Report ◽

Abundance Profile ◽

Microbiome Data

A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual’s microbiome to the growing knowledgebase of “normal” microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and abundances the study also generated a list of contigs of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI’s Short Read Archive.

Download Full-text

Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d’Ivoire

Microorganisms ◽

10.3390/microorganisms9081763 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1763

Author(s):

Veronica Di Cristanziano ◽

Fedja Farowski ◽

Federica Berrilli ◽

Maristella Santoro ◽

David Di Cave ◽

...

Keyword(s):

Gut Microbiota ◽

Cote D'ivoire ◽

Côte D’Ivoire ◽

Enteric Pathogens ◽

Microbiota Composition ◽

Human Gut ◽

Cote D’Ivoire ◽

Human Gut Microbiota ◽

Côte D'ivoire ◽

Gut Microbiota Composition

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d’Ivoire. Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays. Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected. Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis.

Download Full-text