Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients

Lower gastrointestinal tract dysbiosis in persistent critical illness: a systematic review

Introduction. The human lower gastrointestinal tract microbiome is complex, dynamic and prone to disruption occurring during critical illness.Hypothesis or gap statement. The characteristics of lower gastrointestinal tract microbiome disruption and its association with clinical outcomes in patients with prolonged intensive care stay remain uncertain.Aim. To systematically review studies describing lower gastrointestinal tract molecular sequencing in patients with prolonged intensive care stay and explore associations with clinical outcomes.Methodology. This systematic review was prospectively registered and follows the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. OVID MEDLINE, EMBASE and The Cochrane Central Register of Controlled Trials databases were searched for eligible studies describing adults and/or children who underwent molecular sequencing of stool or rectal samples taken on or after 10 days of intensive care.Results. There were 13 studies with 177 patients included. The overall certainty of evidence was low, and no studies reported mortality. Reduced alpha diversity was observed in nine out of nine studies but was not associated with clinical outcomes in four out of four studies. Longitudinal alpha diversity decreased in five out of six studies, and inter-individual beta diversity increased in five out of five studies. After approximately one week of intensive care unit admission, rapid fluctuations in dominant taxa stabilized with trajectories of either recovery or deterioration in five studies. Pathogenic enrichment and commensal depletion were reported in all 13 studies and associated with clinical outcomes in two studies.Conclusion. Lower gastrointestinal tract microbiome disruption is highly prevalent and has consistent characteristics in patients with prolonged intensive care stay. Amongst reported metrics, only relative taxon abundance was associated with clinical outcomes.

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

The prototypic crAssphage (Carjivirus communis) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain its widespread success. Through genomic analyses and culturing, we find that crAssphage uses a phage-plasmid lifestyle to persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, we use a plaque-free culturing approach to measure crAssphage replication in culture with Phocaeicola vulgatus, Phocaeicola dorei, and Bacteroides stercoris, revealing a broad host range. We demonstrate that crAssphage persists with its hosts in culture without causing major cell lysis events or integrating into host chromosomes. The ability to switch between phage and plasmid lifestyles within a wide range of hosts contributes to the prolific nature of crAssphage in the human gut microbiome.

Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Felis catus) using Hi-C proximity ligation and shotgun metagenomics

We used Hi-C proximity ligation with shotgun sequencing to retrieve metagenome-assembled genomes (MAGs) from the fecal microbiomes of two domestic cats (Felis catus). The genomes were assessed for completeness and contamination, classified taxonomically, and annotated for putative antimicrobial resistance (AMR) genes.

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Ganoderma lucidum exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of G. lucidum strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom.

Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning

Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is often low in datasets with a small number of samples due to a lack of robust species co-abundance information. In this study, we exploited the chromatin conformation information obtained from Hi-C sequencing and developed a new reference-independent algorithm, Metagenome Binning with Abundance and Tetra-nucleotide frequencies-Long Range (metaBAT-LR), to improve the binning completeness of these datasets. This self-supervised algorithm builds a model from a set of high-quality genome bins to predict scaffold pairs that are likely to be derived from the same genome. Then, it applies these predictions to merge incomplete genome bins, as well as recruit unbinned scaffolds. We validated metaBAT-LR's ability to bin-merge and recruit scaffolds on both synthetic and real-world metagenome datasets of varying complexity. Benchmarking against similar software tools suggests that metaBAT-LR uncovers unique bins that were missed by all other methods. MetaBAT-LR is open-source and is available at https://bitbucket.org/project-metabat/metabat-lr.

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts

The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.

RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation

Proximity ligation approaches, which are widely used to study the spatial organization of the genome, also make it possible to reveal patterns of RNA-DNA interactions. Here, we use RedC, an RNA-DNA proximity ligation approach, to assess the distribution of major RNA types along the genomes of E. coli, B. subtilis, and thermophilic archaeon T. adornatum. We find that (i) messenger RNAs preferentially interact with their cognate genes and the genes located downstream in the same operon, which is consistent with polycistronic transcription; (ii) ribosomal RNAs preferentially interact with active protein-coding genes in both bacteria and archaea, indicating co-transcriptional translation; and (iii) 6S noncoding RNA, a negative regulator of bacterial transcription, is depleted from active genes in E. coli and B. subtilis. We conclude that the RedC data provide a rich resource for studying both transcription dynamics and the function of noncoding RNAs in microbial organisms.

Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.

BinSPreader: Refine binning results for fuller MAG reconstruction

Despite the recent advances in high-throughput sequencing, metagenome analysis of microbial populations still remains a challenge. In particular, the metagenome-assembled genomes (MAGs) are often fragmented due to interspecies repeats, uneven coverage, and varying strain abundance. MAGs are constructed via a binning process that uses features of input data in order to cluster long contigs presumably belonging to the same species. In this work, we present BinSPreader-a binning refiner tool that exploits the assembly graph topology and other connectivity information to refine binning, correct binning errors, and propagate binning to shorter contigs. We show that BinSPreader could increase the completeness of the bins without sacrificing the purity and could predict contigs belonging to several MAGs. BinSPreader is effective in binning shorter contigs that often contain important conservative sequences that might be of great interest to researchers.