Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut

Abstract

Diet is a major determinant of intestinal microbiome composition. While studies have evaluated microbiome responses to diet variation, less is understood about how the act of feeding influences the microbiome, independent of diet type. Here, we use the clownfish Premnas biaculeatus, a species reared commonly in ornamental marine aquaculture, to test how the diversity, predicted gene content, and gene transcription of the microbiome vary over a 2-day diurnal period with a single daily feeding event. This study used fish fed four times daily, once daily, or every 3 days prior to the diurnal period, allowing us also to test how feeding frequency affected microbiome diversity. The amount of time between feedings had no effect on baseline diversity of the microbiome. In contrast, the act of feeding itself caused a significant short-term change in the microbiome, with microbiome diversity, predicted gene content, and gene transcription varying significantly between time points immediately before and 1.5 hours postfeeding. Variation was driven by abundance shifts involving exact sequence variants (ESVs), with one ESV identified as Photobacterium sp. increasing from <0.5% of sequences immediately prefeeding to 34% at 1.5 h postfeeding. Other ESVs from a range of microbial groups also increased dramatically after feeding, with the majority also detected in the food. One ESV identified as Clostridium perfringens represented up to 55% of sequences but did not vary significantly over the diurnal period and was not detected in the food. Postfeeding samples were enriched in transcripts and predicted genes for social interactions, cell motility, and coping with foreign DNA, whereas time points farther from feeding were enriched in genes of diverse catabolic and biosynthetic functions. These results confirm feeding as a significant destabilizing force in clownfish intestinal microbiomes, likely due to both input of cells attached to food and stimulation of resident microbes. Microbes such as Photobacterium may episodically transition from environmental reservoirs to growth in the gut, likely in association with food particles. This transition may be facilitated by functions for navigating a new environment and interacting with neighboring microbes and host cells. Other taxa, such as Clostridium, are comparatively stable intestinal members and less likely to be affected by passing food. Conclusions about microbiome ecology may therefore differ based on when samples were collected relative to the last feeding. IMPORTANCE Despite extensive study of intestinal microbiome diversity and the role of diet type in structuring gut microbial communities, we know very little about short-term changes in the intestinal microbiome as a result of feeding alone. Sampling microbiomes over a feeding cycle will allow us to differentiate opportunistic, feeding-responsive microbes from resident, potentially commensal members of the gut community. Also, since feeding has the potential to alter microbiome structure, sampling at different points relative to the last feeding event will likely yield different conclusions about microbiome composition and function. This variation should be addressed in comparative microbiome studies. Our study contributes to knowledge of short-term changes in the gut microbiome associated with feeding events.

Fisheries Volume 45 Number 5 May 2020

“…454 pyrosequencing platform. Parris et al 2018 Diet was a major destabilizing event for Clownfi sh gut microbiota, where signifi cant diff erences in microbial communities, predicted gene content, and gene transcription were noted immediately before and 90 min post feeding.…”

Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenileTakifugu obscurus

“…Of note, dosens of ESVs filtered out as chloroplastid were mostly derived from the feed (~13.7% of total reads), but barely detected in gut (~0.1%). Such disproportion indicates that the overrepresent feedborne bacteria in the gut of slow growth fugu were not exclusively due to the influx of DNA from dead or dormant cells (19). Rather, bacteria such as Pseudomonas, optimized to grow at high nutrient as copiotroph (with 6~10 average 16S rRNA copy number) (58), are known to be more competitive than oligotrophy in rapid growing or efficiently utilizing resource in the intestinal environment.…”

“…These findings offer support for our observations that proportions of feed source signals in gut microbiota was negatively correlated with fugu growth rate, which could be largely due to the inconsistent gastric evacuation rate among different sized hosts. Several studies had suggested that the feed associated microbiota could play a crucial role in host health and nutrition (18,19,61), yet little is know about the functional impact and the extent to which it exerted. Herein, BugBase predicted the gut of slow growth fugu (with higher feed source signal) to have significantly more bacteria that are potentially pathogenic and biofilms forming than other fish clusters ( Figure 3).…”

“…The potential niche space in fish gut environment can be determined by the host in multiple ways (17), yet it also can be largely determined by the diet as well as it's associated bacteria (18)(19)(20). Recent findings suggest that a limited numbers of bacterial taxa are shared inter-individually from a given host population and comprise a core gut microbiota (21)(22)(23).…”

“…distinctions in the gut bacterial communties mirrored the environments and vice versa. Especially while considering the abundant bacterial species in the surrounding environments as a potential reservoir (19,33,34). On the other hand, unlike the pond water and sediment, the feed and gut are inherently linked by the high nutrient niche, which might impose a strong environmental selection of microbiota with functional traits linked to copiotroph (13,35).…”