Biology subjects

Humble, J. L.

Publications and source records attributed to Humble, J. L..

4 recordsLinked to original sources

bioRxiv2026

Feed Composition and Antibiotic Supplements Modulate Digestive Enzyme Activities and Alter Gut Microbiome of Pacific White Shrimp

The transition from fishmeal to sustainable alternatives in aquaculture is essential, however the physiological and microbial impacts of alternative diets in shrimp remain poorly understood. Here, we examine how substituting fishmeal with plant-based proteins such as guar and soybean meals, the inclusion of feather meal, and the use of a commonly used antibiotic (gentamicin) influence digestive enzyme function, protein digestibility, and gut microbial assemblages in Litopenaeus vannamei (Pacific white shrimp). The guar-based diet notably altered gut microbiota composition and decreased leucine aminopeptidase activity while maintaining high protein digestibility (>90%). In contrast, the soya/feather diet caused greater disruption to enzyme activity and microbial communities, resulting in reduced digestibility ([~]75%). The gent/guar diet showed comparable digestibility and microbial stability to the guar diet, with only minor shifts at the genus level. Although digestibility data for the acclimation diet were unavailable, these findings highlight diet-specific physiological and microbial responses to fishmeal substitutes. This emphasizes the need to consider dietary formulation, digestive function, and microbiome dynamics when developing sustainable aquafeeds for shrimp farming. ImportanceThe Pacific white shrimp (Litopenaeus vannamei) is a cornerstone of global aquaculture, yet optimizing its diet remains challenging. Current shrimp farming heavily depends on fishmeal, an unsustainable protein source, and antibiotic use to maintain shrimp health raises concerns about antimicrobial resistance and environmental impacts. This study highlights how alternative dietary formulations, including plant-based proteins and antibiotic supplements, influence shrimp digestive physiology and reshape gut microbiomes. Understanding these interactions is crucial to developing feed formulations that support robust shrimp growth and health without excessive reliance on antibiotics or fishmeal. By demonstrating how specific dietary ingredients affect both shrimp digestion and beneficial gut bacteria, this research provides valuable insights that can inform sustainable and responsible shrimp aquaculture practices globally.

microbiology↗

bioRxiv2024

Understanding the Transfer and Persistence of Antimicrobial Resistance in Aquaculture Using a Model Teleost Gut System

The development, progression, and dissemination of antimicrobial resistance (AMR) is determined by interlinked human, animal, and environmental drivers, posing severe risks to human health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. Besides antibiotic judicious use and implementation of antibiotic stewardship programs, mitigating antibiotic resistance spread requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistant plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture. Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors developed for the SalmoSim gut system. The model system was then inoculated with an Escherichia coli strain ATCC 25922 carrying plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L fish feed media for five days prior to a washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including to gram-negative and gram-positive taxa and, crucially, continuing transfer and persistence of the plasmid once florfenicol treatment had been withdrawn. Our findings highlight the role of commensal teleost gut flora as a reservoir for AMR, and our system provides a model to study how different treatment regimes and interventions may be deployed to mitigate AMR persistence.

microbiology↗

bioRxiv2021

Deploying an in vitro gut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-Mos(R) on the Atlantic salmon (Salmo salar) gut microbiome.

Mannose-oligosaccharide (MOS) pre-biotics are widely deployed in animal agriculture as immunomodulators as well as to enhance growth and gut health. Their mode of action is thought to be mediated through their impact on host microbial communities and the associated metabolism. Bio-Mos is a commercially available pre-biotic currently used in the agri-feed industry. To assess Bio-Mos for potential use as a prebiotic growth promotor in salmonid aquaculture, we have modified an established Atlantic salmon in vitro gut model, SalmoSim, to evaluate its impact on the host microbial communities. Inoculated from biological triplicates of adult farmed salmon pyloric caeca compartments, the microbial communities were stabilised in SalmoSim followed by a twenty-day exposure to the prebiotic and in turn followed by an eight day wash out period. Dietary inclusion of MOS resulted in a significant increase in formate (p=0.001), propionate (p=0.037) and isovalerate (p=0.024) levels, correlated with increased abundances of several, principally, anaerobic microbial genera (Fusobacterium, Agarivorans, Pseudoalteromonas). DNA metabarcoding with the 16S rDNA marker confirmed a significant shift in microbial community composition in response to MOS supplementation with observed increase in lactic acid producing Carnobacterium. In conjunction with previous in vivo studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggests that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of in vitro gut models to augment in vivo trials of microbiome modulators. ImportanceIn this paper we report the results of the impact of prebiotic (MOS supplementation) on microbial communities within recently developed Atlantic salmon gut microbiome in vitro simulator. Our data suggest that Bio-Mos may be of value in salmonid production as it enhances volatile fatty acid production in the Atlantic salmon gut and correlates with a significant shift in microbial community composition with observed increase in lactic acid producing Carnobacterium. In conjunction with previous in vivo studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggest that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of in vitro gut models to augment in vivo trials of microbiome modulators.

bioengineering↗

bioRxiv2019

Testing the predictability of morphological evolution in naturally warmed stickleback populations

In light of climate change, the ability to predict evolutionary responses to temperature changes is of central importance for conservation efforts. Prior work has focused on exposing model organisms to different temperatures for just one or a few generations under laboratory conditions. Using a natural experiment, we show that studying parallel evolution in wild populations from contrasting thermal environments presents a more powerful approach for understanding and predicting responses to climate change. More specifically, we used a unique study system in Iceland, where freshwater populations of threespine sticklebacks (Gasterosteus aculeatus) are found in waters warmed by geothermal activity, adjacent to populations in ambient-temperature water. We used three sympatric and three allopatric warm-cold population pairs to test for repeated patterns of morphological divergence in relation to thermal habitat. We found that thermal habitat explained over 50% of body shape variation: fish from warm habitats had a deeper mid-body, a shorter jaw, and smaller eyes. Our common garden experiment showed that most of these morphological differences between thermal habitats were heritable. Lastly, absence of gene flow seems to facilitate parallel divergence across thermal habitats: all three allopatric population pairs were on a common evolutionary trajectory, whereas sympatric pairs followed different trajectories. Our findings therefore suggest that morphological responses to rising temperatures can be predictable when there is limited gene flow. On the other hand, migration of individuals between different thermal habitats or microhabitats can exaggerate nonparallel evolution and reduce our ability to predict evolutionary responses.

evolutionary biology↗