scholarly journals Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Daniel R. Utter ◽  
Gary G. Borisy ◽  
A. Murat Eren ◽  
Colleen M. Cavanaugh ◽  
Jessica L. Mark Welch
Keyword(s):  
Buccal Mucosa ◽  
Habitat Preferences ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
Functional Enrichment ◽  
Habitat Adaptation ◽  
Haemophilus Parainfluenzae ◽  
Population Structures ◽  
Genome Content

Abstract Background The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale. Results Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous. Conclusions Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

scholarly journals Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

2020 ◽  
Author(s):  
Daniel R. Utter ◽  
Gary G. Borisy ◽  
A. Murat Eren ◽  
Colleen M. Cavanaugh ◽  
Jessica L. Mark Welch
Keyword(s):  
Buccal Mucosa ◽  
Habitat Preferences ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
Functional Enrichment ◽  
Habitat Adaptation ◽  
Haemophilus Parainfluenzae ◽  
Population Structures ◽  
Genome Content

AbstractBackgroundThe increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.ResultsHere, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes revealed distinct genomic groups based on shared genome content. H. parainfluenzae genomes separated into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identified an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulated species-level taxonomy and habitat preferences. However, while most R. mucilaginosa were restricted to the tongue as expected, two genomes represented a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identified not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences were absent or ubiquitous.ConclusionsOur findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

scholarly journals Oral Microbiome and Cancer Therapy-Induced Oral Mucositis

2019 ◽  
Vol 2019 (53) ◽  
Author(s):  
Jean-Luc C Mougeot ◽  
Craig B Stevens ◽  
Darla S Morton ◽  
Michael T Brennan ◽  
Farah B Mougeot
Keyword(s):  
Cancer Therapy ◽  
Oral Mucositis ◽  
Human Microbiome ◽  
Holistic Approach ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
Commensal Microbiota ◽  
Intestinal Mucositis

AbstractCharacterization of the role of oral microbiome in cancer therapy-induced oral mucositis (CTOM) is critical in preventing the clinically deleterious effects on patients’ health that are associated with CTOM. Funding initiatives related to the National Institutes of Health human microbiome project have resulted in groundbreaking advancements in biology and medicine during the last decade. These advancements have shown that a human being is in fact a superorganism made of human cells and associated symbiotic or commensal microbiota. In this review, we describe the state of science as it relates to fundamental knowledge on oral microbiome and its role in CTOM. We also discuss how state-of-the-art technologies and systems biology tools may be used to help tackle the difficult challenges ahead to develop effective treatments or preventive therapies for oral mucositis. We make a clear distinction between disease processes pertaining to the oral microbiome, which includes opportunistic pathogens that may be defined as pathobionts, and those infectious disease processes initiated by exogenous pathogens. We also explored the extent to which knowledge from the gastrointestinal tract in disease and intestinal mucositis could help us better understand CTOM pathobiology. Finally, we propose a model in which the oral microbiome participates in the current five-step CTOM pathobiology model. With the advent of more sophisticated metagenomics technologies and methods of analysis, much hope lies ahead to implement an effective holistic approach to treat cancer patients affected by CTOM.

scholarly journals G2S: a new deep learning tool for predicting stool microbiome structure from oral microbiome data

2020 ◽  
Author(s):  
Simone Rampelli ◽  
Marco Candela ◽  
Elena Biagi ◽  
Patrizia Brigidi ◽  
Silvia Turroni
Keyword(s):  
Deep Learning ◽  
Gut Microbiome ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
The Family ◽  
Family Level ◽  
Microbial Metagenomics ◽  
Real Composition ◽  
Microbiome Data

Abstract Background Deep learning methodologies have revolutionized prediction in many fields and show the potential to do the same in microbial metagenomics. However, deep learning is still unexplored in the field of microbiology, with only a few software designed to work with microbiome data. In the frame of meta-community theory, we foresee new perspectives for the development and application of deep learning algorithms in microbiology, with a great potential in the field of human microbiome. Results G2S is a bioinformatic tool for the taxonomic prediction of the human stool microbiome directly from oral microbiome data of the same individual. The tool uses a deep convolutional neural network trained on data of the Human Microbiome Project, allowing to infer the stool microbiome at the family level more accurately than other approaches. G2S was validated on already characterized oral and fecal sample pairs, and then applied to ancient microbiome data from dental calculi, to derive putative intestinal components in medieval subjects. Conclusions G2S infers the family-level taxonomic configuration of the stool microbiome mirroring the real composition with exceptional performance. G2S can be used with modern samples, allowing to predict the eubiotic/dysbiotic state of the gut microbiome when fecal sampling is missing, and especially with ancient samples, as a unique opportunity in the field of paleomicrobiology to recover data related to ancient gut microbiome configurations.

scholarly journals Sequence Comparison of Vaginolysin from Different Gardnerella Species

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 86
Author(s):  
Erin M. Garcia ◽  
Myrna G. Serrano ◽  
Laahirie Edupuganti ◽  
David J. Edwards ◽  
Gregory A. Buck ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Distinct Species ◽  
Vaginal Swab ◽  
Metagenomic Data ◽  
Gardnerella Vaginalis ◽  
Vaginal Epithelial Cells ◽  
Species Specific

Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal epithelial cells and that VLY variation may be one factor that distinguishes less virulent or commensal strains from more virulent strains. This was assessed by bioinformatic analyses of publicly available Gardnerella spp. sequences and quantification of cytotoxicity and cytokine production from purified, recombinantly produced versions of VLY. After identifying conserved differences that could distinguish distinct VLY types, we analyzed metagenomic data from a cohort of female subjects from the Vaginal Human Microbiome Project to investigate whether these different VLY types exhibited any significant associations with symptoms or Gardnerella spp.-relative abundance in vaginal swab samples. While Type 1 VLY was most prevalent among the subjects and may be associated with increased reports of symptoms, subjects with Type 2 VLY dominant profiles exhibited increased relative Gardnerella spp. abundance. Our findings suggest that amino acid differences alter the interaction of VLY with vaginal keratinocytes, which may potentiate differences in bacterial vaginosis (BV) immunopathology in vivo.

scholarly journals Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota

2018 ◽  
Vol 85 (10) ◽  
Author(s):  
Reed M. Stubbendieck ◽  
Daniel S. May ◽  
Marc G. Chevrette ◽  
Mia I. Temkin ◽  
Evelyn Wendt-Pienkowski ◽  
...  
Keyword(s):  
Nasal Cavity ◽  
Iron Acquisition ◽  
Interference Competition ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Siderophore Production ◽  
Coagulase Negative Staphylococci ◽  
Exploitation Competition ◽  
Content Type

ABSTRACTResources available in the human nasal cavity are limited. Therefore, to successfully colonize the nasal cavity, bacteria must compete for scarce nutrients. Competition may occur directly through interference (e.g., antibiotics) or indirectly by nutrient sequestration. To investigate the nature of nasal bacterial competition, we performed coculture inhibition assays between nasalActinobacteriaandStaphylococcusspp. We found that isolates of coagulase-negative staphylococci (CoNS) were sensitive to growth inhibition byActinobacteriabut thatStaphylococcus aureusisolates were resistant to inhibition. AmongActinobacteria, we observed thatCorynebacteriumspp. were variable in their ability to inhibit CoNS. We sequenced the genomes of 10Corynebacteriumspecies isolates, including 3Corynebacterium propinquumisolates that strongly inhibited CoNS and 7 otherCorynebacteriumspecies isolates that only weakly inhibited CoNS. Using a comparative genomics approach, we found that theC. propinquumgenomes were enriched in genes for iron acquisition and harbored a biosynthetic gene cluster (BGC) for siderophore production, absent in the noninhibitoryCorynebacteriumspecies genomes. Using a chrome azurol S assay, we confirmed thatC. propinquumproduced siderophores. We demonstrated that iron supplementation rescued CoNS from inhibition byC. propinquum, suggesting that inhibition was due to iron restriction through siderophore production. Through comparative metabolomics and molecular networking, we identified the siderophore produced byC. propinquumas dehydroxynocardamine. Finally, we confirmed that the dehydroxynocardamine BGC is expressedin vivoby analyzing human nasal metatranscriptomes from the NIH Human Microbiome Project. Together, our results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness.IMPORTANCEWithin the nasal cavity, interference competition through antimicrobial production is prevalent. For instance, nasalStaphylococcusspecies strains can inhibit the growth of other bacteria through the production of nonribosomal peptides and ribosomally synthesized and posttranslationally modified peptides. In contrast, bacteria engaging in exploitation competition modify the external environment to prevent competitors from growing, usually by hindering access to or depleting essential nutrients. As the nasal cavity is a nutrient-limited environment, we hypothesized that exploitation competition occurs in this system. We determined thatCorynebacterium propinquumproduces an iron-chelating siderophore, and this iron-sequestering molecule correlates with the ability to inhibit the growth of coagulase-negative staphylococci. Furthermore, we found that the genes required for siderophore production are expressedin vivo. Thus, although siderophore production by bacteria is often considered a virulence trait, our work indicates that bacteria may produce siderophores to compete for limited iron in the human nasal cavity.

scholarly journals MetaCompass: Reference-guided Assembly of Metagenomes

2017 ◽  
Author(s):  
Victoria Cepeda ◽  
Bo Liu ◽  
Mathieu Almeida ◽  
Christopher M. Hill ◽  
Sergey Koren ◽  
...  
Keyword(s):  
De Novo ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Bacterial Genomes ◽  
Guided Assembly ◽  
Metagenomic Assembly

ABSTRACTMetagenomic studies have primarily relied on de novo approaches for reconstructing genes and genomes from microbial mixtures. While database driven approaches have been employed in certain analyses, they have not been used in the assembly of metagenomes. Here we describe the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods. When combined with de novo assembly approaches, we show that MetaCompass can generate more complete assemblies than can be obtained by de novo assembly alone, and improve on assemblies from the Human Microbiome Project (over 2,000 samples).

scholarly journals Composition of the Oral Microbiome in Patients with Coronary Artery Disease

2020 ◽  
Author(s):  
Thangam Menon ◽  
Supraja Kalyanaraman ◽  
Seethalakshmi Srinivasan
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Bacterial Flora ◽  
Human Microbiome ◽  
Oral Microbiome ◽  
Metagenomic Analysis ◽  
Control Group ◽  
Oral Microbiota ◽  
Normal Human ◽  
Artery Disease

Introduction: Distinct microbial communities reside in the oral cavity and the composition of the oral microbiota has important implications for human health and disease. Identification of bacterial flora of the microbiome is done by metagenomic analysis of 16S ribosomal RNA sequences. Aim: The aim of this study was to characterise the human microbiome in patients with Coronary Artery Disease (CAD) in comparison with the normal human microbiome. Materials and Methods: A pilot study was carried out in tertiary hospital, Chennai. Oral mouthwash samples collected from nine patients with CAD were selected, with one control group. They were studied by metagenomic analysis of V3-V4 region of 16SrRNA gene sequences.. Sequencing of the variable V3 and V4 regions was done using Illumina platform. Results: The six major phyla, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, and Fusobacteriacontained 99% of the taxa in all the samples analysed. Conclusion: Diversity of the microbiome in patients with CAD was similar to the normal human microbiome.

scholarly journals G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Simone Rampelli ◽  
Marco Fabbrini ◽  
Marco Candela ◽  
Elena Biagi ◽  
Patrizia Brigidi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Human Microbiome ◽  
Oral Microbiome ◽  
Fecal Microbiome ◽  
The Family ◽  
Bioinformatic Tool ◽  
Microbial Metagenomics ◽  
Community Theory ◽  
Microbiome Data ◽  
Fecal Sampling

Deep learning methodologies have revolutionized prediction in many fields and show the potential to do the same in microbial metagenomics. However, deep learning is still unexplored in the field of microbiology, with only a few software designed to work with microbiome data. Within the meta-community theory, we foresee new perspectives for the development and application of deep learning algorithms in the field of the human microbiome. In this context, we developed G2S, a bioinformatic tool for taxonomic prediction of the human fecal microbiome directly from the oral microbiome data of the same individual. The tool uses a deep convolutional neural network trained on paired oral and fecal samples from populations across the globe, which allows inferring the stool microbiome at the family level more accurately than other available approaches. The tool can be used in retrospective studies, where fecal sampling was not performed, and especially in the field of paleomicrobiology, as a unique opportunity to recover data related to ancient gut microbiome configurations. G2S was validated on already characterized oral and fecal sample pairs, and then applied to ancient microbiome data from dental calculi, to derive putative intestinal components in medieval subjects.

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