scholarly journals DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome

Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1175 ◽  
Author(s):  
Yihua Sun ◽  
Lingxin Kong ◽  
Guojun Wu ◽  
Bo Cao ◽  
Xiaoyan Pang ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Transcriptional Response ◽  
Fecal Dna ◽  
Human Gut ◽  
Modifying Genes ◽  
Mediators Of Inflammation ◽  
Multiple Characteristics ◽  
Pt Modification ◽  
Chemical Mediators

The DNA phosphorothioate (PT) modification existing in many prokaryotes, including bacterial pathogens and commensals, confers multiple characteristics, including restricting gene transfer, influencing the global transcriptional response, and reducing fitness during exposure to chemical mediators of inflammation. While PT-containing bacteria have been investigated in a variety of environments, they have not been studied in the human microbiome. Here, we investigated the distribution of PT-harboring strains and verified their existence in the human microbiome. We found over 2000 PT gene-containing strains distributed in different body sites, especially in the gastrointestinal tract. PT-modifying genes are preferentially distributed within several genera, including Pseudomonas, Clostridioides, and Escherichia, with phylogenic diversities. We also assessed the PT modification patterns and found six new PT-linked dinucleotides (CpsG, CpsT, ApsG, TpsG, GpsC, ApsT) in human fecal DNA. To further investigate the PT in the human gut microbiome, we analyzed the abundance of PT-modifying genes and quantified the PT-linked dinucleotides in the fecal DNA. These results confirmed that human microbiome is a rich reservoir for PT-containing microbes and contains a wide variety of PT modification patterns.

scholarly journals Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

2020 ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Biological Information ◽  
Complex Environment ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
Genes Encoding ◽  
Biological Entities ◽  
Relevant Degree

Abstract Background: Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits. Results: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.Conclusions: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.

scholarly journals Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

2020 ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Biological Information ◽  
Complex Environment ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
Genes Encoding ◽  
Biological Entities ◽  
Relevant Degree

Abstract Background: Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits. Results: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.Conclusions: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.

scholarly journals Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

2020 ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Biological Information ◽  
Complex Environment ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
Genes Encoding ◽  
Biological Entities ◽  
Relevant Degree

Abstract Background: Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits. Results: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.Conclusions: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.

scholarly journals Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Biological Information ◽  
Complex Environment ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
Genes Encoding ◽  
Biological Entities ◽  
Relevant Degree

Abstract Background Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits. Results In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life. Conclusions The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.

scholarly journals De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments

2019 ◽  
Author(s):  
Bahar Behsaz ◽  
Hosein Mohimani ◽  
Alexey Gurevich ◽  
Andrey Prjibelski ◽  
Mark F. Fisher ◽  
...  
Keyword(s):  
Natural Products ◽  
Gastrointestinal Tract ◽  
Cyclic Peptides ◽  
De Novo ◽  
Genome Mining ◽  
Human Microbiome ◽  
Important Class ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Bioactive Natural Products

ABSTRACTCyclic and branch cyclic peptides (cyclopeptides) represent an important class of bioactive natural products that include many antibiotics and anti-tumor compounds. However, little is known about cyclopeptides in the human gut, despite the fact that humans are constantly exposed to them. To address this bottleneck, we developed the CycloNovo algorithm for de novo cyclopeptide sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms. CycloNovo reconstructed many new cyclopeptides that we validated with transcriptome, metagenome, and genome mining analyses. Our benchmarking revealed a vast hidden cyclopeptidome in the human gut and other environments and suggested that CycloNovo offers a much-needed step-change for cyclopeptide discovery. Furthermore, CycloNovo revealed a wealth of anti-microbial cyclopeptides from food that survive the complete human gastrointestinal tract, raising the question of how these cyclopeptides might affect the human microbiome.SIGNIFICANCEThe golden age of antibiotics was followed by a decline in the pace of antibiotics discovery in the 1990s. The key prerequisite for the resurgence of antibiotics research is the development of a computational discovery pipeline for antibiotics sequencing. We describe such pipeline for cyclic and branch cyclic peptides (cyclopeptides) that represent an important class of bioactive natural products such as antibiotics and anti-tumor compounds. Our CycloNovo algorithm for cyclopeptide sequencing reconstructed many new cyclopeptides that we validated with transcriptome, metagenome, and genome mining analyses. CycloNovo revealed a wealth of anti-microbial cyclopeptides from food that survive the complete human gastrointestinal tract, raising the question of how these cyclopeptides might affect the human microbiome.

scholarly journals Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

2020 ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Biological Information ◽  
Complex Environment ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
Genes Encoding ◽  
Biological Entities ◽  
Relevant Degree

Abstract Background: Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits. Results: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.Conclusions: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.

scholarly journals Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

2020 ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Biological Information ◽  
Complex Environment ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
Genes Encoding ◽  
Biological Entities ◽  
Relevant Degree

Abstract Background: Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits. Results: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.Conclusions: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.

scholarly journals Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?

2020 ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Human Microbiome ◽  
Ecological Role ◽  
Complex Environment ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
Genes Encoding ◽  
Biological Entities ◽  
Relevant Degree

Abstract Background: Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits. Results: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life. Conclusions : The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating information about their metabolic propensity and ecological role in a complex environment like the human gastrointestinal tract.

scholarly journals The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Melinda A. Engevik ◽  
Heather A. Danhof ◽  
Anne Hall ◽  
Kristen A. Engevik ◽  
Thomas D. Horvath ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Metabolic Pathways ◽  
Glycosyl Hydrolase ◽  
Acid Resistance ◽  
Human Gut ◽  
Nutrient Sources ◽  
Metabolic Plasticity ◽  
Defined Media ◽  
High Viability ◽  
Ph Range

Abstract Background Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium dentium. Results B. dentium displayed acid resistance, with high viability over a pH range from 4 to 7; findings that correlated to the expression of Na+/H+ antiporters within the B. dentium genome. B. dentium was found to adhere to human MUC2+ mucus and harbor mucin-binding proteins. Using microbial phenotyping microarrays and fully-defined media, we demonstrated that in the absence of glucose, B. dentium could metabolize a variety of nutrient sources. Many of these nutrient sources were plant-based, suggesting that B. dentium can consume dietary substances. In contrast to other bifidobacteria, B. dentium was largely unable to grow on compounds found in human mucus; a finding that was supported by its glycosyl hydrolase (GH) profile. Of the proteins identified in B. dentium by proteomic analysis, a large cohort of proteins were associated with diverse metabolic pathways, indicating metabolic plasticity which supports colonization of the dynamic gastrointestinal environment. Conclusions Taken together, we conclude that B. dentium is well adapted for commensalism in the gastrointestinal tract.

scholarly journals Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron

2015 ◽  
Vol 81 (12) ◽  
pp. 3973-3983 ◽  
Author(s):  
Alicia Lammerts van Bueren ◽  
Aakanksha Saraf ◽  
Eric C. Martens ◽  
Lubbert Dijkhuizen
Keyword(s):  
Gastrointestinal Tract ◽  
Carbohydrate Metabolism ◽  
Lactobacillus Reuteri ◽  
Bacterial Species ◽  
Transport Systems ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Positive Health ◽  
Content Type ◽  
Commensal Species

ABSTRACTProbiotic microorganisms are ingested as food or supplements and impart positive health benefits to consumers. Previous studies have indicated that probiotics transiently reside in the gastrointestinal tract and, in addition to modulating commensal species diversity, increase the expression of genes for carbohydrate metabolism in resident commensal bacterial species. In this study, it is demonstrated that the human gut commensal speciesBacteroides thetaiotaomicronefficiently metabolizes fructan exopolysaccharide (EPS) synthesized by probioticLactobacillus reuteristrain 121 while only partially degrading reuteran and isomalto/malto-polysaccharide (IMMP) α-glucan EPS polymers.B. thetaiotaomicronmetabolized these EPS molecules via the activation of enzymes and transport systems encoded by dedicated polysaccharide utilization loci specific for β-fructans and α-glucans. Reduced metabolism of reuteran and IMMP α-glucan EPS molecules may be due to reduced substrate binding by components of the starch utilization system (sus). This study reveals that microbial EPS substrates activate genes for carbohydrate metabolism inB. thetaiotaomicronand suggests that microbially derived carbohydrates provide a carbohydrate-rich reservoir forB. thetaiotaomicronnutrient acquisition in the gastrointestinal tract.

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