Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor

DeMaere, Matthew Z.; Liu, Michael Y. Z.; Lin, Enmoore; Djordjevic, Steven P.; Charles, Ian G.; Worden, Paul; Burke, Catherine; Monahan, Leigh G.; Gardiner, Melissa; Borody, Thomas J.; Darling, Aaron E.

doi:10.1128/mra.01523-19

Cited by 10 publications

(9 citation statements)

References 11 publications

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“…The distribution of meta3C reads along the longest contigs (> 100 Kb) of the different assemblies confirms that most of the PE reads correspond to "shotgun"-like reads, with very few useful trans, or long-range cis contacts (Figure 1-figure supplement 1b). These 3D ratios compare favorably to those obtained in recently published works, including using commercial solutions that encompass a biotin enrichment step (compare with 0.36% and 2.38% from DeMaere et al, 2020;Press et al, 2017 respectively), but they remain weak overall.…”

Section: High-quality Proximity Ligation Meta3c Libraries Of Human Gut Microbiomesupporting

confidence: 83%

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Marbouty

Thierry

Millot

et al. 2021

eLife

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Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6,000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarter of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high-specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.

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Section: High-quality Proximity Ligation Meta3c Libraries Of Human Gut Microbiomesupporting

confidence: 83%

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Marbouty

Thierry

Millot

et al. 2021

eLife

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“…Previous studies have implemented 3C/Hi-C-based methods on the gut microbiome of humans and animals [21][22][23][24]28]. In this this study, we sought to implement meta3C on a human stool sample to link ARGs to their microbial hosts, as well as compare the 3C data generated here to previously published 3C/Hi-C datasets with the aim to optimise analysis methods for 3C/Hi-C data by reducing the impact of spurious intercontig reads.…”

Section: Discussionmentioning

confidence: 99%

“…3C/Hi-C approaches have been used to considerable effect in improving the assembly of MAGs in complex microbial ecosystems such as those present in the bovine rumen [17], the gut of dogs [18], sheep [19] and pigs [20]. Several studies have been performed using 3C/Hi-C to study the human gut microbiota [21][22][23][24][25]. The overarching goal of this study was to explore whether meta3C and Hi-C can be used to reliably link ARGs to their microbial hosts.…”

Section: Figure 1 Metagenomic Chromosome Conformation Capture Approachesmentioning

confidence: 99%

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

McCallum

Rossiter

Quraishi

et al. 2022

Preprint

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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 repetitive 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 for spurious links, 87 ARGs were linked 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 encoding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.

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“…These systems form a foundation for genome-focused studies across the domain, keeping in mind that some MAGs suffer from data quality problems not encountered in sequences from cultured organisms (Garg et al, 2020), particularly when closely related strains cohabitate and confound existing assembly and binning methods (Sczyrba et al, 2017). Problems related to MAG binning fidelity of short read assemblies are increasingly solved by including long-read sequencing data to produce hybrid assemblies (Frank et al, 2016;Xie et al, 2020;Ciuffreda et al, 2021), by utilizing Hi-C to assay the physical proximity of DNA sequences (DeMaere et al, 2020), and by employing single-cell genomics (Stepanauskas, 2012;Rinke et al, 2013;Pachiadaki et al, 2019).…”

Section: Outlook On Archaeal Research and Global Cooperationmentioning

confidence: 99%

Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea

et al. 2022

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Editorial on the Research Topic Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea ECOLOGY OF ARCHAEA IN "NON-EXTREME" MARINE ENVIRONMENTSSeveral papers in the Research Topic explore the ecology of archaea in marine environments. These studies are framed by a perspective article by Ed DeLong on planktonic marine archaea (DeLong). The perspective chronicles the exciting discovery in the 1990s by DeLong and contemporaries that

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Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor

Abstract: We report the availability of a high-quality metagenomic Hi-C data set generated from a fecal sample taken from a healthy fecal microbiome transplant donor subject. We report on basic features of the data to evaluate their quality.

Cited by 10 publications

References 11 publications

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

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

Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea

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