Biology subjects

Degregori, S.

Publications and source records attributed to Degregori, S..

5 recordsLinked to original sources

bioRxiv2026

Ubiquitous trophic niche partitioning drives species coexistence and biomass on coral reefs

Coral reefs support an extraordinary diversity and biomass of fishes. However, whether species coexist through fine-scale niche partitioning, and whether this impacts ecosystem functioning, remain unresolved. We combined DNA metabarcoding and stable isotope analysis to reconstruct a high-resolution food web and quantify the trophic niches of 2,060 reef fishes across 261 species. We observed extreme trophic partitioning: species pairs diverged by a median of 93% (DNA metabarcoding) and 86% (stable isotopes), consistently overlapping far less than expected by chance. Further, communities with greater trophic complementarity supported higher standing-stock biomass, particularly at high species richness. Our results confirm limiting similarity and trophic complementarity as the driving forces of coexistence and ecosystem functioning in the ocean's most diverse ecological community.

ecology↗

bioRxiv2026

An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution

Animal gut microbiomes provide key physiological functions and are critical for host health. They vary dramatically across the animal kingdom, and are shaped by factors including host diet, evolutionary history and environment. However, analyses of gut microbiomes spanning the entire metazoan clade are lacking, limiting our understanding of the fundamental principles governing gut microbiomes. Here we present the Gut Microbiome Tree of Life (GMToL), a curated 16S amplicon dataset of 17,366 samples from 1,553 host species across 26 host classes from 284 studies, enabling analysis of large-scale evolutionary trends. Using ancestral state reconstruction, we provide a critical baseline calculation of major compositional shifts in gut microbiomes throughout animal evolution. We show that the ancestral animal gut was likely dominated by Pseudomonadota. A major shift to Bacteroidota occurred during the evolution of tetrapods, followed by the emergence of Bacillota-dominated guts in mammals and birds. We identify conserved core gut microbes and demonstrate how GMToL can be leveraged to contextualize the evolutionary history of specific microbial taxa. Ultimately, this framework enables the predictive mapping of microbial symbionts across uncharacterized host lineages, and establishes a quantitative baseline for comparative microbiome research at scale.

microbiology↗

bioRxiv2026

Enabling Megascale Microbiome Analysis with DartUniFrac

We introduce a new algorithm, DartUniFrac, and a near-optimal implementation with GPU acceleration, up to three orders of magnitude faster than the state of the art and scaling to millions of samples (pairwise) and billions of taxa. DartUniFrac connects UniFrac with weighted Jaccard similarity and exploits sketching algorithms for fast computation. We benchmark DartUniFrac against exact UniFrac implementations, demonstrating that DartUniFrac is statistically indistinguishable from them on real-world microbiome and metagenomic datasets.

bioinformatics↗

bioRxiv2025

The microbiome of the human facial skin is unique compared to that of other hominids

The human facial skin microbiome is remarkably similar across all people sampled to date, dominated by facultative anaerobe Cutibacterium. The origin of this genus is unknown, with no close relatives currently described from samples of primate skin. This apparent human-specific bacterial taxon could reflect the unique nature of human skin, which is significantly more oily than that of our closest primate relatives. However, previous studies have not sampled the facial skin microbiome of our closest primates. Here, we profiled the skin microbiome of zoo-housed chimpanzees (Pan troglodytes), and gorillas (Gorilla gorilla gorilla), alongside their human care staff, using both 16S and shotgun sequencing. We showed that facial skin microbiomes differ significantly across host species, with humans having the lowest diversity and most unique community among the three species. We were unable to find a close relative of Cutibacterium on either chimpanzee or gorilla facial skin, consistent with human-specificity. Hominid skin microbiome functional profiles were more functionally similar compared to their taxonomic profiles. However, we still found notable functional differences including lower proportions of fatty acid biosynthesis on humans, consistent with microbes reliance on host-derived lipids. Our study highlights the uniqueness of the human facial skin microbiome and supports a horizontal acquisition of its dominant resident from a yet unknown source. ImportanceUnderstanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts distinct bacteria--particularly Cutibacterium acnes--we did not know if these bacteria and their associated genes were also present on the faces of our closest relatives, chimpanzees and gorillas. Our study shows that human facial skin hosts markedly different bacteria than other primates, with C. acnes being uniquely abundant on human faces. This finding suggests that this key bacterial species may have adapted specifically to human skin, which produces more oils than other primates.

microbiology↗

bioRxiv2021

Firmicutes and Bacteroidetes explain mass gain variation in an obligate hibernator

O_LIBody condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. C_LIO_LIIt is well documented that symbiotic microorganisms play a vital role in animal physiology and behaviour. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity; Firmicutes is consistently associated with obesity while Bacteroidetes is associated with leanness both in humans and other animals. C_LIO_LIThe focus of most microbiome studies has been on human health or involved lab reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. C_LIO_LIHere we test whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes are associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by quantifying microbial abundance over five years of fecal samples (2015 - 2019) collected during their summer active season. C_LIO_LIResults show that marmots with higher mass gain rates have a greater abundance of Firmicutes. In contrast, higher abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates, and similarly in harsher environments. C_LIO_LIAlthough correlative, these results highlight the importance of symbiotic gut microbiota to mass gain in the wild, a trait associated with survival and fitness in many taxonomic groups. C_LI

microbiology↗