Advances and Challenges in Understanding the Virosphere
by Prof. Robert Edwards
The viruses that prey on bacteria sculpt and shape every microbiome. Recent innovations in viral metagenomics are unveiling the roles of viruses in controlling bacterial populations, contributing to disease, and promoting health. Hecatomb is an end-to-end pipeline optimised to extract viral genomes from metagenomic samples. With an emphasis on QC, host-removal, and avoiding using large datasets, we designed hecatomb to use computational resources efficiently. Phables is a new approach we developed to identify complete phage genomes from metagenomes and to allow the reconstruction of strain-level viral genomes. The biggest challenge for viral metagenomics remains the annotation of proteins, and some of the new machine-learning approaches released recently are revolutionising our understanding of the virus world. We will also discuss the problems and challenges in understanding how viruses influence the microbiome.
Prof. Robert Edwards is a Matthew Flinders Fellow in Bioinformatics at College of Science and Engineering, Flinders University, Australia. He received his PhD from the University of Sussex, UK. His postdoctoral experiences across various U.S. institutions resulted in considerable advancements in genome annotation and virus-host interactions. At San Diego State University, he achieved notable breakthroughs, including identifying a globally prevalent virus and exploring metagenomics of coral reefs.
Prof. Edwards has published over 100 scientific papers, and has taught both microbiology and computer science for over 20 years. He has earned over $10m in extramural funding to support his research. He was elected to the American Academy of Microbiology and nominated a Kavli Frontiers Fellow by the National Academy of Sciences.
Prof. Edwards is the Director of Bioinformatics and Human Microbiology for the Flinders Accelerator for Microbiome Exploration (FAME). He coordinates the computational analysis of DNA sequences associated with the microbiome. Although Prof. Edwards’s research focus is on the human microbiome, he has also published work on many different environments.
Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease
Allergic diseases affect millions of people worldwide. An increase in their prevalence has been associated with alterations in the gut microbiome, i.e., the microorganisms and their genes within the gastrointestinal tract. Maturation of the infant immune system and gut microbiota occur in parallel; thus, the conformation of the microbiome may determine if tolerant immune pro- gramming arises within the infant. Here we show, using deeply phenotyped participants in the CHILD birth cohort (n = 1115), that there are early-life influences and microbiome features which are uniformly associated with four distinct allergic diagnoses at 5 years: atopic dermatitis (AD, n = 367), asthma (As, n = 165), food allergy (FA, n = 136), and allergic rhinitis (AR, n = 187). In a subset with shotgun metagenomic and metabolomic profiling (n = 589), we discover that impaired 1-year microbiota maturation may be universal to pediatric allergies (AD p = 0.000014; As p = 0.0073; FA p = 0.00083; and AR p = 0.0021). Extending this, we find a core set of functional and metabolic imbalances characterized by compromised mucous integrity, elevated oxida- tive activity, decreased secondary fermentation, and elevated trace amines, to be a significant mediator between microbiota maturation at age 1 year and allergic diagnoses at age 5 years (β indirect = −2.28; p = 0.0020). Microbiota maturation thus provides a focal point to identify deviations from normative development to predict and prevent allergic disease.
Department of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada.
Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
Link to OA paper: https://www.nature.com/articles/s41467-023-40336-4
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut
Clostridioides difficile colonizes up to 30-40% of community-dwelling adults without causing disease. C. difficile infections (CDIs) are the leading cause of antibiotic-associated diarrhea in the U.S. and typically develop in individuals following disruption of the gut microbiota due to antibiotic or chemotherapy treatments. Further treatment of CDI with antibiotics is not always effective and can lead to antibiotic resistance and recurrent infections (rCDI). The most effective treatment for rCDI is the reestablishment of an intact microbiota via fecal microbiota transplants (FMTs). However, the success of FMTs has been difficult to generalize because the microbial interactions that prevent engraftment and facilitate the successful clearance of C. difficile are still only partially understood. Here we show how microbial community-scale metabolic models (MCMMs) accurately predicted known instances of C. difficile colonization susceptibility or resistance. MCMMs provide detailed mechanistic insights into the ecological interactions that govern C. difficile engraftment, like cross-feeding or competition involving metabolites like succinate, trehalose, and ornithine, which differ from person to person. Indeed, three distinct C. difficile metabolic niches emerge from our MCMMs, two associated with positive growth rates and one that represents non-growth, which are consistently observed across 14,862 individuals from four independent cohorts. Finally, we show how MCMMs can predict personalized engraftment and C. difficile growth suppression for a probiotic cocktail (VE303) designed to replace FMTs for the treatment rCDI. Overall, this powerful modeling approach predicts personalized C. difficile engraftment risk and can be leveraged to assess probiotic treatment efficacy. MCMMs could be extended to better understand personalized engraftment of other opportunistic bacterial pathogens, beneficial probiotic organisms, or more complex microbial consortia.
Institute for Systems Biology, University of Washington, USA
Link to preprint: https://www.biorxiv.org/content/10.1101/2023.04.28.538771v2.abstract
No evidence for a common blood microbiome based on a population study of 9,770 healthy humans
Human blood is conventionally considered sterile but recent studies suggest the presence of a blood microbiome in healthy individuals. Here we characterized the DNA signatures of microbes in the blood of 9,770 healthy individuals using sequencing data from multiple cohorts. After filtering for contaminants, we identified 117 microbial species in blood, some of which had DNA signatures of microbial replication. They were primarily commensals associated with the gut (n = 40), mouth (n = 32) and genitourinary tract (n = 18), and were distinct from pathogens detected in hospital blood cultures. No species were detected in 84% of individuals, while the remainder only had a median of one species. Less than 5% of individuals shared the same species, no co-occurrence patterns between different species were observed and no associations between host phenotypes and microbes were found. Overall, these results do not support the hypothesis of a consistent core microbiome endogenous to human blood. Rather, our findings support the transient and sporadic translocation of commensal microbes from other body sites into the bloodstream.
Genome Institute of Singapore, Singapore
Link to OA paper: https://www.nature.com/articles/s41564-023-01350-w
Probing the Metatranscriptome of the House Mosquito Culex tritaeniorhynchus from the Philippines
Culex tritaeniorhynchus is a common household mosquito vector for arboviruses and filarial parasites. To circumvent the development of insecticide resistance, untargeted metatranscriptomics approaches in studying local Culex microbiomes can unveil potential paratransgenic vectors and critical host-microbiome interaction gene targets, serving as foundations for alternative vector biosurveillance and control methods. The metatranscriptomes generated from house mosquitoes collected from Barangays Bayog and Lalakay, Los Baños, Laguna, were pre-processed and host-filtered via fastp, bowtie2, and OpenContami. The clean dscDNA reads were then pooled per barangay and assembled using Trinity and metaSPAdes. Bacterial metatranscripts were retrieved for blastx annotation against the UniProt database, GO and KEGG analysis, and STRING protein-protein interaction network generation. Gram-negative bacterial genera Escherichia, Shigella, and Pseudomonas traceable to the local aquatic and human microflora chiefly contributed to the abundance of transcripts involved in antimicrobial resistance, secondary metabolite transport, aromatic amino acid biosynthesis, cell wall organization, genome regulation, two-component signaling, and iron cofactor metabolism.
Eight candidate prokaryotic genes were selected based on relative abundance and relevance to virulence, xenobiotic metabolism, and other adaptive functions. In both barangays and in select individual mosquitoes, all eight candidate genes were validated via RT-qPCR, exhibiting a wide range of Ct values and melt curve profiles. Genes involved in sustained survival against mosquito innate immune processes (enolases, peptidases, LPS remodelers) posit key players essential for the fitness of a potential paratransgenic vector. Individual variation in RT-qPCR detection results may hint at the relationship between the local and internal environments with respect to Culex microbiomes. As a pioneering metatranscriptomics study in the Philippines, we present potentially culturable paratransgenic vectors for Culex vector control, molecular mechanisms relevant to Culex-microbiome “interactomics”, and the role of environments in mediating the virulence of Culex parasites and symbionts. Recommendations include bacterial mRNA-enriched extraction protocols, in silico workflow integration with meta-omics datasets, and in vitro validation of culturable bacterial symbionts and their respective genes relevant for vector control.
National Institute of Molecular Biology and Biotechnology - University of the Philippines Diliman, Philippines
Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift
The majority of studies that focus on the connection between gut microbiota and obesity often encounter conflicting results, casting doubt on the reliability of the observed patterns. Additionally, the specific species responsible for driving changes in gut microbiota associated with obesity and whether these findings can be replicated remain unexplored. To address these questions, we conducted an extensive analysis of gut microbial metagenome sequencing data, aiming to gain a deeper understanding of the interaction between obese individuals and their gut microbiota. We collected and examined data from 3329 samples, including 1494 from obese individuals and 1835 from control subjects, originating from 17 different countries. This dataset encompassed both 16S rRNA gene and metagenomic sequence data.
We employed a machine-learning approach to curate, profile, and combine fecal metagenomic data from diverse geographical locations, with the goal of identifying consistent global patterns associated with obesity. We initiated our investigation by assessing whether alterations in the microbial community structure could serve as a distinguishing feature of the obese gut microbiome. Our findings consistently revealed a reduction in diversity within the gut microbiome of obese individuals compared to their lean counterparts. This loss of diversity appears to be responsible for disruptions in the healthy functional capabilities of the microbial community.
Through our analysis, we pinpointed 25 highly predictive microbial species and identified 37 pathways associated with obesity, which served as distinctive signatures. These signatures were subsequently validated with a high degree of accuracy (AUC, Species: 0.85, and Pathway: 0.80) using an independent validation dataset. Notable observations include a decrease in producers of short-chain fatty acids (such as several Alistipes species and Odoribacter splanchnicus) and a reduction in microbes that promote gut barrier integrity (like Akkermansia muciniphila and Bifidobacterium logum) in the obese gut.
Our analysis emphasized the importance of pathways related to short-chain fatty acid production, purine and pyrimidine biosynthesis, and carbohydrate metabolism in control individuals. In contrast, obese individuals exhibited enrichment in pathways related to amino acids, enzyme cofactors, and peptidoglycan biosynthesis. Furthermore, we identified contributors to key functional shifts associated with obesity, which were found to be both specific to the dataset and shared across multiple datasets.
National Institute of Technology Durgapur, India