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

2019 ◽  
Author(s):  
Matteo Soverini ◽  
Simone Rampelli ◽  
Silvia Turroni ◽  
Patrizia Brigidi ◽  
Elena Biagi ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Original Study ◽  
Rrna Gene ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Minimal Set ◽  
A Genome ◽  
Genes Encoding ◽  
Relevant Degree ◽  
The 16S Rrna Gene

Abstract Background. Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shot-gut sequencing techniques. Such approach has been proposed as a mean to discover new so-called ‘uncultured metagenomic species’. Results. In the present analysis we compare 400 genomes from isolates available on NCBI database and 400 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. Even if a genome completeness up to 96% is reported in the original study, the metagenomic species resulted substantially depleted in genes encoding for essential functions to support autonomous bacterial life, with the 16S rRNA gene missing in 237 out of the 400 metagenomic species we analyzed. Conclusions. The relevant degree of lacking core functionalities that we observed in metagenomic species raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating information about their metabolic propensity and ecological role in 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 Biochemical traits that Escherichia coli evolved during its adaption to the gastrointestinal tract of humans

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Escherichia Coli ◽  
Gastrointestinal Tract ◽  
Selection Pressure ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Multiple Sequence ◽  
E Coli ◽  
Starting Point ◽  
Altered Gene ◽  
Different Strains

What biochemical tricks did Escherichia coli obtained or evolved during its time as a commensal in the human gastrointestinal system? E. coli is a natural symbiont of the human gastrointestinal tract. Thus, through evolutionary timescales, the bacterium must have co-evolved with humans with conditions in the gastrointestinal tract serving as selection pressure for the evolution of a variety of biochemical and physiological adaptations. These adaptations came about through mutations that arise in the genome, and thus, could be retrospectively profiled to understand the differing evolutionary pressure that selected for specific traits in the bacterium useful for its survival in the changing conditions of the human gut. Using sequenced and annotated genome information of different strains of E. coli as a guide and starting point, possibility exists to use a combination of bioinformatics, biochemical, and genetic approaches to decipher the biochemical tricks that E. coli evolved or pick up during its time as a commensal in the human gastrointestinal tract. Specifically, sequenced genomes serve as a molecular fossil from which we could obtain imprints of the various evolutionary events that impact on the bacterium. Adaptations to changing conditions could also be deciphered through analysis of single nucleotide polymorphism (SNPs). Comparison of the profiled mutations and altered gene sequences between different E. coli strains with different co-evolutionary history with the human gut might help reveal the different length of time in which different E. coli strains have co-evolved with humans. More importantly, multiple sequence alignment and phylogenetic analysis could also reveal which genes first evolve due to selection pressure exerted on the bacterium by fluctuating environmental conditions in the human gut. Genetic knockdowns of the putative genes would help indicate the overall essentiality of the genes to the physiology and functioning of the modern E. coli bacterium. The approach outlined should help answer some of the most fundamental questions regarding the evolution of different E. coli strains as well as how natural selection exerts its influence on the physiology of a commensal organism with respect to host adaptation.

scholarly journals A comprehensive analysis of the global human gut archaeome from a thousand genome catalogue

2020 ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Alexander Mahnert ◽  
Guillaume Borrel ◽  
Alexandre Almeida ◽  
Almut Werner ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Novel Species ◽  
The Novel ◽  
Archaeal Diversity ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Separate Species ◽  
Genomic Features ◽  
Substantial Correlation ◽  
Health And Disease

The human gut microbiome plays an important role in health and disease, but the archaeal diversity therein remains largely unexplored. Here we report the pioneering analysis of 1,167 non-redundant archaeal genomes recovered from human gastrointestinal tract microbiomes across countries and populations. We identified three novel genera and 15 novel species including 52 previously unknown archaeal strains. Based on distinct genomic features, we warrant the split of the Methanobrevibacter smithii clade into two separate species, with one represented by the novel Candidatus M. intestini. Patterns derived from 1.8 million proteins and 28,851 protein clusters coded in these genomes showed a substantial correlation with socio-demographic characteristics such as age and lifestyle. We infer that archaea are actively replicating in the human gastrointestinal tract and are characterized by specific genomic and functional adaptations to the host. We further demonstrate that the human gut archaeome carries a complex virome, with some viral species showing unexpected host flexibility. Our work furthers our current understanding of the human archaeome, and provides a large genome catalogue for future analyses to decipher its role and impact on human physiology.

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