The human gut virome: inter-individual variation and dynamic response to diet.

By S. Minot, Rohini Sinha, Jun Chen, Hongzhe Li, S. Keilbaugh, Gary D. Wu, James D. Lewis, Frederic D. Bushman. Genome Research, 2011

901 citations recorded by the source corpus.

Immense populations of viruses are present in the human gut and other body sites. Understanding the role of these populations (the human "virome") in health and disease requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we investigate viromes from human subjects on a controlled feeding regimen. Longitudinal fecal samples were analyzed by metagenomic sequencing of DNA from virus-like particles (VLP) and total microbial communities. Assembly of 336 Mb of VLP sequence yielded 7175 contigs, many identifiable as complete or partial bacteriophage genomes. Contigs were rich in viral functions required in lytic and lysogenic growth, as well as unexpected functions such as viral CRISPR arrays and genes for antibiotic resistance. The largest source of variance among virome samples was interpersonal variation. Parallel deep-sequencing analysis of bacterial populations showed covaration of the virome with the larger microbiome. The dietary intervention was associated with a change in the virome community to a new state, in which individuals on the same diet converged. Thus these data provide an overview of the composition of the human gut virome and associate virome structure with diet.

Subfields: Ecology, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cfef00bab9d840102b9fb2eb91079b2200ca4058

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Infectious Diseases

In Molecular Biology

Citations in the corpus

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota (2017, background): “Interestingly, it has been shown that individuals who follow the same dietary habits have a tendency to harbor a similar virome, likely reflecting a diet-dependent microbiota, allowing the proliferation of phages infecting the more dominant members of this microbiota (483).”
CRISPR-Cas Systems: RNA-mediated Adaptive Immunity in Bacteria and Archaea (2013, background): “CRISPR arrays have also been located in free viral genomes (Minot et al. 2011; García-Heredia et al. 2012) and in small Sulfolobus conjugative plasmids pNOB8 and pKEF9 (She et al. 1998; Greve et al. 2004).”
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (2017, background): “For example, viral sequences were estimated to comprise 4 – 17% of human gut prokaryote metagen-omes [7].”
The human gut virome is highly diverse, stable and individual-specific (2019, background): “Similar to the bacteriome, the gut virome also displays high inter-individual and 48 low intra-individual variation (Minot et al., 2011).”
The Impact of the Gut Microbiota on Human Health: An Integrative View (2012, positive): “Similar to gut bacteria, interpersonal variation in the virome is high (Minot et al., 2011; Reyes et al., 2010).”
Computational approaches to predict bacteriophage–host relationships (2015, background): “Thus far, metagenomic analysis has revealed the genomes of many new phages and unexpected distributions of known ones (Minot et al. 2011, 2013; McCallin et al. 2013; Mizuno et al. 2013b; Dutilh et al. 2014; Aziz et al. 2015).”
Disease-specific Alterations in the Enteric Virome in Inflammatory Bowel Disease (2015, methodology): “Comparison across cohorts revealed that enteric viromes were unique between individuals and between cohorts, which is consistent with previous reports on the incredible diversity of the human gut virome (Minot et al., 2011; Reyes et al., 2010).”
Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents (2013, background): “Recently changes in bacteriophage communities in gut have been correlated with dietary interventions [5].”
Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study (2017, background): “In healthy individuals, the gut virome is highly stable over time [23, 47, 69], with some phage populations hypothesized to provide a non-hostderived protective barrier to invading bacterial pathogens [70, 71].”
Mechanisms and consequences of intestinal dysbiosis (2017, background): “Because lysogenic bacteriophages dominate the human gut [172, 173], phage sequences are mainly embedded as prophage DNA in bacterial chromosomes.”
From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome (2012, background): “Likewise, we do not devote a lot of attention to viruses as researchers are only now beginning to document the diversity of viruses found in the human body and their role in the human microbiome (e.g., Minot et al. 2011, Reyes et al. 2010).”