The gut virome of the protochordate model organism, Ciona intestinalis subtype A

Highlights

• The gut virome of the protochordate model organism, Ciona intestinalis subtype A.

• Ciona possesses a gut virome distinct from seawater.

• Ciona maintain temporally stable viruses.

• The Ciona gut virome is dominated by viruses from the Caudovirales order.

• Bacteria and viruses exhibit compartmentalization in the stomach, mid- and hindgut.

Abstract

The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members. Comparison of gut tissues before and after starvation in virus-free water enabled the differentiation between the Ciona-specific virome and transient viral communities associated with dietary sources. The Ciona gut viromes were dominated by double-stranded DNA tailed phages (Order Caudovirales) and sequence assembly yielded a number of complete circular phage genomes, most of which were highly divergent from known genomes. Unique viral communities were found in distinct gut niches (stomach, midgut and hindgut), paralleling the compartmentalization of bacterial communities. Additionally, integrase and excisionase genes, including many that are similar to prophage sequences within the genomes of bacterial genera belonging to the Ciona core microbiome, were prevalent in the viromes, indicating the active induction of prophages within the gut ecosystem. Knowledge of the gut virome of this model organism lays the foundation for studying the interactions between viruses, bacteria, and host immunity.

Introduction

In recent years, numerous studies have defined the importance of host-associated microorganisms, including both bacteria and viruses. The bacterial component of this ‘microbiome’ often outnumbers host cells by an order of magnitude (Turnbaugh et al., 2007) and can influence host nutrient acquisition and metabolism (Nicholson et al., 2012, Tremaroli and Backhed, 2012). The increased recognition of the contributions of bacterial communities to the biology and physiology of animals has motivated our perception of animals as complex metaorganisms (Rohwer et al., 2002, Rosenberg and Zilber-Rosenberg, 2011, Theis et al., 2016). This concept was first introduced into biology to describe the coral animal and all of its associated microbes (Rohwer et al., 2002). Since then, many animal models, including humans, have been documented to contain a stable, core community of bacteria on or within their bodies (Dishaw et al., 2014, Roeselers et al., 2011, Sabree et al., 2012, Schmitt et al., 2012, Turnbaugh and Gordon, 2009), the disruption of which often results in disease (Cho and Blaser, 2012, Sobhani et al., 2011, Tamboli et al., 2004). While bacteria have historically predominated microbiome studies, recent efforts are recognizing a vital role for viruses as well (Abeles and Pride, 2014, Grasis et al., 2014, Minot et al., 2011, Reyes et al., 2010, Thurber et al., 2017). The viruses associated with animal hosts are present as both free viral particles and/or stably integrated proviruses (Feschotte and Gilbert, 2012) and can shape the health of the metaorganism through pathogenesis (Davies et al., 2016) or through influencing the metabolic potential of both the animal host and its associated microbes (Roossinck, 2011). In addition to host immunity (Cullender et al., 2013, Thaiss et al., 2016), nutrient availability (Cohen et al., 2015), and bacterial competition (Flint et al., 2007), viruses, the majority of which are bacteriophages (i.e. phages), likely affect the structure of animal-associated bacterial communities through lytic infection and prophage integration and/or induction. In this report, we describe the gut virome of a marine filter-feeding invertebrate protochordate, Ciona intestinalis subtype A, cataloging for the first time the viral communities associated with these early extant chordates and establishing a tractable model system in which to pursue future studies examining the complex dynamics between metazoan hosts and their associated bacterial and viral communities.

Ciona is a well-known developmental model system that has been adapted recently for studies of host-microbe interactions within the gut ecosystem (Dishaw et al., 2014, Dishaw et al., 2011, Dishaw et al., 2016, Liberti et al., 2014). This animal is a marine filter-feeding protochordate that derives nutrients from particulates in the water column, including phytoplankton (Coleman, 1991). Ciona is amenable to germ-free mariculture (Leigh et al., 2016) and has been shown previously to maintain a core bacterial community in its gut (Dishaw et al., 2014). Here we report the presence of temporally stable viruses within this metabolically active environment. We also describe evidence for compartmentalization of both viruses and bacteria, with distinct members occupying the stomach, midgut, and hindgut. The observation that Ciona maintains a virome with many predicted hosts matching members of the core microbiome and a prevalence of prophages indicates a role for phages as major players in shaping host-associated bacterial communities within the dynamic gut ecosystem of these animals.