Biology subjects

Martin, J. P.

Publications and source records attributed to Martin, J. P..

5 recordsLinked to original sources

bioRxiv2026

Fecal metabolomics reveals preferential complex carbohydrate utilization and guides cultivation of murine gut Firmicutes

The murine gut microbiota provides robust colonization resistance against Clostridioides difficile infection (CDI), yet murine-associated microbes remain notoriously difficult to cultivate in vitro, limiting mechanistic investigation. To identify the ecological and nutritional basis of this cultivation barrier, we leveraged CDI susceptibility as a functional readout of microbial community metabolism to infer in vivo nutrient utilization. Germ-free C57BL/6 mice colonized with varying dilutions of ethanol-treated murine microbiota were challenged with C. difficile resulting in a spectrum of CDI outcomes. Comparative metabolomics of pre-challenge fecal samples revealed a consistent carbohydrate signature: glucose accumulated in communities that resisted C. difficile challenge, whereas complex carbohydrates, including raffinose, sucrose, trehalose, lactose, sorbitol, and mannitol, were significantly depleted. The broad depletion of these complex carbohydrates supports their functional importance within the collective microbial community. Conventional glucose-based media (CMA, BHI+I, RCMT) failed to support robust growth or subculture of murine gut microbiota. Guided by the metabolomics findings, we developed Peptone Yeast Extract with Six Salts and Sugars (PYE6S), a glucose-free medium supplemented with the complex carbohydrates identified as depleted. PYE6S enabled cultivation of 22 unique Firmicutes ASVs, 82% of which lacked named cultured representatives in reference databases. These findings suggest a plausible explanation for why conventional media fail and support a metabolomics-guided framework for rational cultivation of host-associated microbiota across diverse systems. This strategy may be extended to guide media design for other host-associated microbiotas.

microbiology↗

bioRxiv2024

The geometry of prey capture in praying mantis forelegs

The form of an animals limbs has to balance multiple functions: locomotion, grasping, climbing, and jumping, among others. For cryptic animals, especially those that resemble elements of their habitat like sticks or grasses, the limbs may also be modified to enhance the camouflage. The performance of a limb in one category may require a tradeoff, reducing performance in another category. Praying mantises provide a diverse group of insects who all use their forelegs for one function, capturing prey, while some species use them as part of their camouflage. Here we use a large database of images of mantis species to capture the variation in morphology across the order, and to calculate the largest prey that their forelegs can hold. We find that the length and thickness of the femur and the length of the tibia comprise most of the variability across species. The majority of species have similar foreleg morphology, with two large groups extending into areas of the morphospace with thicker or thinner forelegs. A geometric relationship between dimensions of the foreleg and the optimal prey diameter maps directly onto the variability across species determined by principal components analysis; legs with thinner femurs and shorter tibia cant hold large prey, and the distribution of the species across the morphospace follows the gradient of optimum prey size. These results suggest that some species trade ability to grasp larger prey for benefits including crypsis, and the praying mantises are an ideal system for studying morphological and functional variation in limbs.

zoology↗

bioRxiv2024

A new leaf sensing organ in a predatory insect group, the praying mantises (Mantodea)

Animals sensory systems enable them to navigate and interact with their environments. Adaptive specializations of these systems can generate novel structures or organs that support highly unique niche adaptations. We report the discovery of a novel sensory organ in a group of praying mantises (Insecta, Mantodea, Nanomantoidea), which have an unusual "leaf-planking" ecomorphic life strategy, laying against the undersides of broadleaf vegetation. Histology, scanning electron microscopy, and x-ray computed tomography all support the novelty of this distinct morphology while electrophysiology reveals that the sensory organ, herein designated the gustifolium organ, detects plant volatiles. The location of the gustifolium organon the ventral thoracic surface of these mantises appears to facilitate the chemical detection of the leaves on which it resides. The gustifolium is a novel plant volatile-detecting sensory structure in an obligate predatory insect, directly linked to a newly-identified, highly-adapted life strategy.

zoology↗

bioRxiv2022

Dynamic Kinetic Models Capture Cell-Free Metabolism for Improved Butanol Production

Cell-free systems are useful tools for prototyping metabolic pathways and optimizing the production of various bioproducts. Mechanistically-based kinetic models are uniquely suited to analyze dynamic experimental data collected from cell-free systems and provide vital qualitative insight. However, to date, dynamic kinetic models have not been applied with rigorous biological constraints or trained on adequate experimental data to the degree that they would give high confidence in predictions and broadly demonstrate the potential for widespread use of such kinetic models. In this work, we construct a large-scale dynamic model of cell-free metabolism with the goal of understanding and optimizing butanol production in a cell-free system. Using a novel combination of parameterization methods, the resultant model captures experimental metabolite measurements across two experimental conditions for nine metabolites at timepoints between 0 and 24 hours. We present analysis of the model predictions, provide recommendations for butanol optimization, and identify the aldehyde/alcohol dehydrogenase as the primary bottleneck in butanol production. Sensitivity analysis further reveals the extent to which various parameters are constrained, and our approach for probing valid parameter ranges can be applied to other modeling efforts.

synthetic biology↗

bioRxiv2019

Extreme storm-induced run-off causes rapid, context-dependent shifts in nearshore subtropical bacterial communities

Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment--locally known as red soil pollution--and caused moderate increases of macronutrients--especially SiO2 and PO43-. We detected shifts in relative abundances of marine bacteria and the introduction of terrestrially-derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.

microbiology↗