scholarly journals Separation of Cohorts on the Basis of Bacterial Type IV Conjugation Systems Identified From Metagenomic Assemblies

2021 ◽  
Author(s):  
Benjamin R Joris ◽  
Tyler S Browne ◽  
Thomas A Hamilton ◽  
David R Edgell ◽  
Gregory B Gloor
Keyword(s):  
North American ◽  
Gut Microbiome ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Term Infants ◽  
Human Gut Microbiome ◽  
Type Iv ◽  
Shotgun Metagenomic Sequencing ◽  
Age Related ◽  
Inflammatory Bowel

Abstract BackgroundConjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identification of these systems in metagenomic samples clinically important. ResultsHere, we outline two distinct methods to identify conjugative elements in the human gut microbiome. We first show that conjugative elements exhibit strong population and age-level stratification. Furthermore, the taxonomic compositions of the conjugative elements differ from the composition of the metagenome assembled genomes, both in terms of the number of assembled elements and the relative abundances of the assembled systems. Finally, we demonstrate that the majority of assembled conjugative elements are not included within metagenomic bins, and that only a small proportion of the binned conjugative systems are included in "high-quality" metagenomic bins. Our findings highlight that conjugative systems differ between a North American inflammatory bowel disease cohort and a cohort of North American pre-term infants, but in a manner different than metagenome assembled genomes, revealing a potential use as an age-related biomarker. Additionally, conjugative systems can distinguish between other geographical-based cohorts. ConclusionsAnalysis of the human gut microbiome by shotgun metagenomic sequencing has revealed numerous connections to human health outcomes. Our findings emphasize the need to identify and analyze conjugative systems outside of standard metagenomic binning pipelines. We suggest that analysis of type IV conjugative systems should be added to the current metagenomic analysis approaches as they contain much information that could explain differences between cohorts beyond those we investigated.

scholarly journals Separation of cohorts on the basis of bacterial type IV conjugation systems identified from metagenomic assemblies

2021 ◽  
Author(s):  
Benjamin R Joris ◽  
Tyler S Browne ◽  
Thomas A Hamilton ◽  
David R Edgell ◽  
Gregory B Gloor
Keyword(s):  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Human Gut ◽  
Term Infants ◽  
Human Gut Microbiome ◽  
North Americans ◽  
Type Iv ◽  
Age Related ◽  
Bacterial Type ◽  
Potential Use

Conjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identification of these systems in metagenomic samples clinically important. Here, we outline two distinct methods to identify conjugative systems in the human gut microbiome. We first show that conjugative systems exhibit strong population and age-level stratification. Additionally, we find that the total relative abundance of all conjugative systems present in a sample is not an informative metric to use, regardless of the method of identifying the systems. Finally, we demonstrate that the majority of assembled conjugative systems are not included within metagenomic bins, and that only a small proportion of the binned conjugative systems are included in "high-quality" metagenomic bins. Our findings highlight that conjugative systems differ between general North Americans and a cohort of North American pre-term infants, revealing a potential use as an age-related biomarker. Furthermore, conjugative systems can distinguish between other geographical-based cohorts. Our findings emphasize the need to identify and analyze conjugative systems outside of standard metagenomic binning pipelines.

scholarly journals A unique and reliable fecal DNA extraction method for 16S rRNA gene and shotgun metagenomic sequencing in the analysis of the human gut microbiome

2020 ◽  
Author(s):  
Céline Elie ◽  
Magali Perret ◽  
Karen Louis ◽  
Asmaà Fritah-Lafont ◽  
Philippe Leissner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Shotgun Metagenomic Sequencing

Abstract Background: The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to select a unique and best performing DNA extraction protocol for both metagenomic sequencing methods. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) in order to facilitate DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and sequenced with both metagenomic methods. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates.Results: Independently of the sequencing methods used, SPD significantly improved efficiency of the four tested protocols compared with their commercial version, in terms of extracted DNA quality, accuracy of the predicted composition of the microbiota (notably for Gram-positive bacteria), sample alpha-diversity, and experimental repeatability. The best overall performance was obtained for the S-DQ protocol, SPD combined to the DNeasy PowerLyser PowerSoil protocol from QIAGEN.Conclusion: Based on this evaluation, we recommend to use the S-DQ protocol, to obtain standardized and high quality extracted DNA in the human gut microbiome studies.

scholarly journals Dynamics of the human gut microbiome in inflammatory bowel disease

2017 ◽  
Vol 2 (5) ◽  
Author(s):  
Jonas Halfvarson ◽  
Colin J. Brislawn ◽  
Regina Lamendella ◽  
Yoshiki Vázquez-Baeza ◽  
William A. Walters ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Inflammatory Bowel

scholarly journals Interplay between the human gut microbiome and host metabolism

2019 ◽  
Author(s):  
Alessia Visconti ◽  
Caroline I. Le Roy ◽  
Fabio Rosa ◽  
Niccolo Rossi ◽  
Tiphaine C. Martin ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Taxonomic Composition ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Metabolic Potential ◽  
Microbial Ecosystem ◽  
Microbiome Composition ◽  
Shotgun Metagenomic Sequencing ◽  
Key Species

AbstractThe human gut is inhabited by a complex and metabolically active microbial ecosystem regulating host health. While many studies have focused on the effect of individual microbial taxa, the metabolic potential of the entire gut microbial ecosystem has been largely under-explored. We characterised the gut microbiome of 1,004 twins via whole shotgun metagenomic sequencing (average 39M reads per sample). We observed greater similarity, across unrelated individuals, for functional metabolic pathways (82%) than for taxonomic composition (43%). We conducted a microbiota-wide association study linking both taxonomic information and microbial metabolic pathways with 673 blood and 713 faecal metabolites (Metabolon, Inc.). Metabolic pathways associated with 34% of blood and 95% of faecal metabolites, with over 18,000 significant associations, while species-level results identified less than 3,000 associations, suggesting that coordinated action of multiple taxa is required to affect the metabolome. Finally, we estimated that the microbiome mediated a crosstalk between 71% of faecal and 15% of blood metabolites, highlighting six key species (unclassified Subdoligranulum spp., Faecalibacterium prausnitzii, Roseburia inulinivorans, Methanobrevibacter smithii, Eubacterium rectale, and Akkermansia muciniphila). Because of the large inter-person variability in microbiome composition, our results underline the importance of studying gut microbial metabolic pathways rather than focusing purely on taxonomy to find therapeutic and diagnostic targets.

Age-related prevalence of Methanomassiliicoccus luminyensis in the human gut microbiome

Apmis ◽  
2012 ◽  
Vol 120 (10) ◽  
pp. 773-777 ◽  
Author(s):  
Bédis Dridi ◽  
Mireille Henry ◽  
Hervé Richet ◽  
Didier Raoult ◽  
Michel Drancourt
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Age Related

scholarly journals Selecting age-related functional characteristics in the human gut microbiome

Microbiome ◽  
2013 ◽  
Vol 1 (1) ◽  
pp. 2 ◽  
Author(s):  
Yemin Lan ◽  
Andres Kriete ◽  
Gail L Rosen
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Functional Characteristics ◽  
Human Gut Microbiome ◽  
Age Related

scholarly journals Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 331
Author(s):  
Nachon Raethong ◽  
Massalin Nakphaichit ◽  
Narissara Suratannon ◽  
Witida Sathitkowitchai ◽  
Wanlapa Weerapakorn ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Asian Country ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Thai Population ◽  
Shotgun Metagenomics ◽  
Human Gut Microbiome ◽  
Metabolic Functions

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

scholarly journals The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhongyu Mou ◽  
Yiyan Yang ◽  
A. Brantley Hall ◽  
Xiaofang Jiang
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Human Gut ◽  
Taxonomic Distribution ◽  
Human Gut Microbiome ◽  
Endogenous Histamine ◽  
Histamine Production ◽  
Significant Enrichment ◽  
Inflammatory Bowel

Abstract Background Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria. Results To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog. Using bioinformatic approaches, we identified 117 putative histamine-secreting bacteria species. A new three-component decarboxylation system including two colocalized decarboxylases and one transporter was observed in histamine-secreting bacteria among three different phyla. We found significant enrichment of histamine-secreting bacteria in patients with inflammatory bowel disease but not in patients with colorectal cancer suggesting a possible association between histamine-secreting bacteria and inflammatory bowel disease. Conclusions The findings of this study expand our knowledge of the taxonomic distribution of putative histamine-secreting bacteria in the human gut.

scholarly journals Consumption of Fermented Plant Foods Is Associated with Systematic Differences in the Human Gut Microbiome and Metabolome

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1573-1573
Author(s):  
Nicole Litwin ◽  
Bryn Taylor ◽  
Franck Lejzerowicz ◽  
Marion Poirel ◽  
Justin Shaffer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Food Consumption ◽  
Gut Microbiome ◽  
Amplicon Sequencing ◽  
Fermented Foods ◽  
Metagenomic Sequencing ◽  
Plant Food ◽  
Gut Health ◽  
Human Gut ◽  
Human Gut Microbiome

Abstract Objectives Fermented foods have gained much attention due to their proposed gut health benefits from recent clinical trials. However, very few studies have explored the effects of fermented foods, especially of plant origin, on gut microbiota composition and functional capacity in large human cohorts. Thus, the objective of this study was to assess whether self-reported fermented plant food consumption is associated with compositional or functional microbiome changes in a subset of individuals in the American Gut Project (AGP) cohort. Methods Using a multi-omics approach (e.g., 16S rRNA amplicon sequencing, metagenomic sequencing, and untargeted mass spectrometry), we analyzed stool samples from 6811 healthy individuals from the AGP including 115 individuals specifically recruited for their fermented plant food consumption for a targeted four-week longitudinal study. Results We observed subtle, yet statistically significant differences between fermented plant food consumers and non-consumers in beta diversity as well as differential taxa between the two groups. We found that the metabolome of fermented plant food consumers was enriched with conjugated linoleic acid (CLA), a putatively health-promoting compound. Cross-omic analyses between metagenomic sequencing and mass spectrometry suggest that CLA may be driven by taxa associated with fermented plant food consumers. Conclusions Collectively, we found modest, yet persistent signatures associated with fermented plant food consumption that appear present in multiple omic types, which motivates further investigation of how different types of fermented foods may impact the human gut microbiome and overall health. Funding Sources Danone Nutricia Research.

scholarly journals Biomass distances from personalized multispecies dynamic flux balance analysis of the human gut microbiome identify dietary influences for patients with and without inflammatory bowel disease

2019 ◽  
Author(s):  
Alexandros C. Dimopoulos ◽  
Martin Reczko
Keyword(s):  
Inflammatory Bowel Disease ◽  
Flux Balance Analysis ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Dynamic Flux Balance Analysis ◽  
Flux Balance ◽  
Balance Analysis ◽  
Inflammatory Bowel

A parallelized version of a multispecies dynamic flux balance analysis (msdFBA) algorithm is implemented and applied to the AGORA collection of genome-scale metabolic reconstructions for 818 members of the human gut microbiome. The msdFBA method assumes the well stirred interaction mode of all organisms to exchange external metabolites. In each msdFBA simulation, the biomasses the gut microbiome composition of one of 149 patients from NIH Human Microbiome Project is used for initialization in combination with one of 11 different diets used as substrates as defined in the Virtual Metabolic Human database. The union of all species in the patient data comprises 255 different microbes. The patients are either healthy or suffer from inflammatory bowel disease (IBD). The msdFBA simulation is performed for 50 time steps. For all combinations of patients and time steps, the euclidean distance between the vector of the biomasses of the 255 patient species and the evolving vector of biomasses for the same species is calculated, providing the information about the biomass distance to each patient during each simulation. To quantify the overall influence of a diet for all patients, a diet score is defined as the sum of the reciprocal distances to the closest patient at the last time step, in case the closest patient is diseased, subtracted from the respective sum for the case that the closest patient is healthy. With this score, the known beneficial influences both of a high fiber and a gluten free diet for IBD is verified. Noteworthy is the utility of a Mediterranean diet in this context, having similar distance patterns. The proposed method provides an universal platform for the in-silico analysis of different environmental influences like diets for different microbiotas defined by metagenomic quantifications from individual patients and has the potential to generate additional dietary recommendations for the management of various other diseases.

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