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Consistent, Scale-Dependent Differences in the Biogeography of Host-Associated and Free-Living Microbiomes Across
Joshua H Dominguez1, Andreas Härer1, Christopher B Wall1,2
1Department of Ecology, Behavior, and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, California, USA.
Molecular Ecology
|June 13, 2026
Summary
Host-associated microbes in fish guts show different spatial patterns and diversity than free-living lake microbes. Host association fundamentally alters microbial distribution, highlighting the need to include hosts in microbial biogeography studies.
Area of Science:
- Ecology
- Microbial Ecology
- Biogeography
Background:
- Microbial communities are essential for ecosystem functions and host evolution.
- Understanding differences between host-associated and free-living microbes remains limited.
Purpose of the Study:
- To compare metacommunity structure, spatial turnover, and neutral theory adherence between fish gut and lake bacterioplankton microbes.
- To investigate how host association influences microbial diversity and spatial distribution.
Main Methods:
- 16S amplicon sequencing to characterize microbial communities.
- Comparison of alpha and beta diversity, spatial turnover (distance-decay), and neutral abundance-occurrence models.
- Study conducted across two lake systems with different fish species.
Main Results:
- Fish gut microbiomes exhibited lower alpha diversity but higher within-lake beta diversity than bacterioplankton.
- Bacterioplankton showed stronger spatial turnover with distance and were more consistent across lakes.
- Neutral models explained bacterioplankton but not fish-associated microbial communities.
Conclusions:
- Host-associated and free-living microbes display distinct metacommunity structures and spatial turnover patterns.
- Host association significantly alters microbial diversity and spatial distribution, suggesting strong local selection or limited microbial exchange among hosts.
- Observed patterns were consistent across different lake systems, indicating widespread effects of host association on microbial biogeography.
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