Assessing the validity of fecal sampling for characterizing variation in threespine stickleback’s gut microbiota

PLOS ONE · 5 authors, 2 centres

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TL;DR

This study compared bacterial communities from intestinal tissue and feces in threespine stickleback fish. It found that while there are some differences, fecal samples largely overlap with gut tissue samples and can successfully detect microbiota shifts due to a diet change, suggesting fecal sampling is a viable non-lethal method.

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Researchers also tested if fecal sampling could detect microbiota shifts caused by an experimental diet manipulation. The results showed significant differences between sample types and temporal variation among fecal samples, yet the bacterial communities largely overlapped, sharing a median of 90.3% of bacterial communities. Host population explained a larger proportion of variance (10.7%) than sample type (5.9%). The authors conclude that fecal sampling can be an adequate non-lethal method for characterizing the stickleback gut microbiota and studying temporal dynamics, but note limitations like small sample size (n=7) and high temporal variation, recommending temporal replicates and environmental sampling for future studies.

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other

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preclinical research

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ORIGINAL PAPER

PMC10513271

Assessing the validity of fecal sampling for characterizing variation in threespine stickleback’s gut microbiota

PLOS ONE

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ABSTRACT

Abstract The gut microbiota is crucial for many aspects of their hosts’ biology, and it has been characterized for many species across the animal kingdom. Yet, we still don’t have a good understanding of whether non-lethal sampling can accurately capture the diversity of gut-associated bacterial communities, as estimated from lethal sampling of intestinal tissue. We further lack knowledge on whether non-lethal sampling methods are suitable for detecting gut microbiota shifts associated with changes in environmental factors (e.g., diet). We addressed these questions in threespine stickleback fish, a model system for evolutionary ecology, by comparing bacterial communities from intestinal tissue and feces. Despite some differences in community composition between the two sample types and considerable temporal variation among fecal samples, bacterial communities appear to largely overlap. Further, we detected consistent and significant changes of fecal bacterial communities associated with an experimental diet manipulation. This suggests that fecal sampling can represent an adequate non-lethal method to characterize the gut microbiota of threespine stickleback, but additional studies will be necessary before drawing general conclusions regarding the validity of fecal sampling for gut microbiota studies. To this end, we give recommendations to improve the characterization of the gut microbiota via fecal sampling. Fecal sampling allows studying temporal gut microbiota shifts associated with environmental change at the individual level, which increases opportunities for future experimental gut microbiota research.

CITATION EXPORT

Andreas Härer, Diana J Rennison, Rina Bagsic Opulencia et al.. Assessing the validity of fecal sampling for characterizing variation in threespine stickleback’s gut microbiota. PLOS ONE. (2023). https://doi.org/10.1371/journal.pone.0290875

AUTHORS

5 · 2 CENTRES

Andreas Härer, Diana J Rennison, Rina Bagsic Opulencia, Rina Bagsic Opulencia, Rina Bagsic Opulencia

1School of Biological Sciences, Department of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, California, United States of America
2Institute of Biological Sciences, University of the Philippines, PHILIPPINES