Biology subjects

Arnoldini, M.

Publications and source records attributed to Arnoldini, M..

13 recordsLinked to original sources

bioRxiv2026

Quantifying Chemical Fluxes Underlying Gut Microbiota-Host Interactions

To resolve how the gut microbiota shapes human health, it is essential to quantify the exchange of chemicals between microbes and the host. Much as the dose of a drug determines its pharmacological effect, the magnitude of a specific chemical flux determines its impact. Here, we establish from first principles how fluxes can be estimated by integrating key parameters from human digestive physiology and microbial metabolism. We apply this framework to three cases: the exchange of fermentation products, the production of toxins by bacterial pathogens, and nitrogen homeostasis. Our analysis identifies three directly measurable host-level parameters which, in concert with microbial activity, shape flux magnitudes: intestinal transit time, absolute microbial abundance in feces, and fecal mass loss. The simultaneous quantification of these parameters provides a feasible yet essential step toward a mechanistic and quantitative description of gut microbiota-host interactions across health and disease.

systems biology↗

bioRxiv2026

Comprehensive analysis of ammonia and biogenic amines in ecologically diverse systems with high-resolution mass spectrometry

The acquisition of sufficient nitrogen for growth, as well as the disposal of highly toxic nitrogen-containing degradation products, represent serious metabolic challenges in all multicellular organisms and microbial ecosystems. Understanding these processes requires a broadly applicable system to accurately quantify the concentration of a wide spectrum of biological amines and inorganic nitrogen-containing compounds. To date, this has been challenging due to limited specificity, selectivity, breadth and/or sensitivity of assays. Here we present a simple, optimized method based on liquid chromatography and high-resolution mass spectrometry, with an accompanying analysis pipeline, for the accurate quantification of more than 30 of these compounds, including ammonia. We demonstrate the effectiveness of this method in quantifying relevant nitrogen-containing compounds in mouse and human gut content, bacterial cultures, algal symbiosis in a cnidarian and freshwater ecosystem samples. As a proof-of-concept, we applied the method to study the influence of the gut microbiome on cecal nitrogen distribution in mice with different gnotobiotic microbiomes. This revealed a profound influence of gut microbiota composition on amino acid, ammonia, and amine concentrations in the upper large intestine. Overall, we provide a broadly applicable approach that can be used across microbial ecology fields to generate novel insights into the biology of nitrogen assimilation, exchange, and disposal.

microbiology↗

bioRxiv2025

Transcriptomic profiles of single-copy marker genes enable predicting bacterial growth states in microbial communities

Studying microbial community dynamics is fundamental to better understand ecosystem stability, resilience and environmental change. Community composition changes with the growth of individual members, yet current methods to estimate microbial growth in communities face substantial limitations. For example, genome sequence-based estimates of maximum growth rates may not reflect growth patterns in the natural environment well, and metagenomic in situ growth prediction requires the availability of reference genomes and shows limited accuracy for slow-growing bacteria. Gene expression data provide an information-rich readout of community activity that could reflect growth, however, cross-species comparisons in community settings remain challenging. An approach using expression signatures of universal, single-copy marker genes provides independence from reference genomes and may thereby enable comparability across species. Here, we present a transcriptomic, marker gene-based growth classifier that predicts the growth states of bacterial strains from different phyla cultivated in diverse conditions. We demonstrate its application in vivo in gnotobiotic mice carrying the same bacterial strains, and in a more complex synthetic community, where predicted growth states align with reported growth inhibition induced by systemic inflammatory response. This approach offers a new method for predicting bacterial growth states across species, with potential for broad application in the study of microbial growth dynamics at the whole community level.

microbiology↗

bioRxiv2025

Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions

Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine cecum, resulting from growth within the gel-like structure of cecum content, and periodic disruption due to peristalsis-driven shear-thinning and clearance. Shear-thinning can also explain the surprising observation that fed beads enter the tip of the mouse cecum by flow along the epithelial cell layer before being mixed into the cecum content. Our study shows mechanistically how spatial structure in the gut emerges through the interplay of microbial and host physiology and highlights the possibility of host control over gut microbiota distribution via gut contractions. One sentence summaryWe show how spatial structure emerges in the gut microbiota through bacterial growth in the matrix of gut content.

systems biology↗

bioRxiv2024

Quantifying the daily harvest of fermentation products from the human gut microbiota

Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2-5% of human energy demand for Western, and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiotas mechanistic functions in health and disease.

microbiology↗

bioRxiv2023

The differing prevalences of propionate and butyrate producing bacteria in the human gut microbiota

Propionate and butyrate are major fermentation products released during the anaerobic growth of bacteria in the large intestine with strong implications on host health. While the different metabolic pathways leading to the release of these products are biochemically well characterized, less is known about their relative abundances across hosts and conditions. Here, we introduce a bioinformatics pipeline which connects pathway analyses, gene identification via sequence homology, and the screening of metagenomic samples to systematically identify the abundances of propionate producing pathways across individuals and in relation to butyrate producing pathways. We found that on average 36% of all genomes of a gut microbiota carried propionate producing pathways with the sodium-pumping succinate pathway being the most prevalent. This pathway abundance was anti-correlated to the abundance of butyrate pathways and greatly depended on host physiology. For example, propionate pathway abundance varied strongly among infants with a substantially higher abundance in vaginally than C-section born infants, increased in early adulthood, and decreased again with higher ages. This is in strong contrast to the known variation of butyrate pathway abundance, which is close to zero in infants and steadily increases with age. These results highlight the contrasting prevalence of both fermentation products at the individual level with shifts in microbiota composition resulting in strong consequences on the amount of butyrate and propionate available to the host.

microbiology↗

bioRxiv2023

Nanoscale clustering by O-antigen-Secretory Immunoglobulin-A binding limits outer membrane diffusion by encaging individual Salmonella cells

Secreted immunoglobulins, predominantly SIgA, influence the colonization and pathogenicity of mucosal bacteria. While part of this effect can be explained by SIgA-mediated bacterial aggregation, we have an incomplete picture of how SIgA binding influences cells independently of aggregation. Here we show that akin to microscale crosslinking of cells, SIgA targeting the Salmonella Typhimurium O-antigen extensively crosslinks the O-antigens on the surface of individual bacterial cells at the nanoscale. This crosslinking results in an essentially immobilized bacterial outer membrane. Membrane immobilization, combined with Bam-complex mediated outer membrane protein insertion results in biased inheritance of IgA-bound O-antigen, concentrating SIgA-bound O-antigen at the oldest poles during cell growth. By combining empirical measurements and simulations, we show that this SIgA-driven biased inheritance increases the rate at which phase-varied daughter cells become IgA-free: a process that can accelerate IgA escape via phase-variation of O-antigen structure. Our results show that O-antigen-crosslinking by SIgA impacts workings of the bacterial outer membrane, helping to mechanistically explain how SIgA may exert aggregation-independent effects on individual microbes colonizing the mucosae.

microbiology↗

bioRxiv2023

Acute targeted induction of gut-microbial metabolism disrupts host circadian rhythm

The gut microbiota and host diurnal rhythm mutually influence each other, and microbiota metabolism has been shown to play a role in regulating host circadian function via secretion of fermentation products. Microbial metabolism is dependent on the availability of nutrients for the microbiota, typically through the hosts food intake, making it challenging to disentangle the effect of host and microbiota metabolism. In this study, we acutely induced gut microbial metabolic activity without inducing host metabolism in mice. We found that increasing microbial metabolism in the gut altered clock gene expression locally. Actuating microbiota metabolism also reduced host food intake beyond the calories provided by the microbiota, suggesting a systemic signaling effect of microbial metabolism on the host.

microbiology↗

bioRxiv2022

Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota

Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. However, we remain largely blind to the quantitative effects of processes determining colonization success. In this study, we used genetically-barcoded Bacteroides thetaiotaomicron (B.theta) strains in combination with mathematical modeling to quantify population bottlenecks experienced by B.theta during gut colonization. Integrating population bottlenecks sizes with careful quantification of net growth rates in vivo and in vitro allows us to build models describing the events during intestinal colonization in the context of gnotobiotic and complex microbiotas. Using these models, we estimated the decrease in niche size for B.theta colonization with increasing microbiota complexity. In addition, our system can be applied to mechanistically dissect colonization defects of mutant strains. As a proof of concept, we demonstrated that the competitive disadvantage of a B.theta mutant lacking capsular polysaccharide is due to a combination of an increased lag-phase before growth initiation in the gut, combined with an increased clearance rate. Crucially, the requirement for the B.theta capsule depended strongly on microbiota composition, suggesting that the dominant role may be protection from bacterial or phage aggression rather than from host-induced bactericidal mechanisms.

microbiology↗

bioRxiv2022

Non-invasive monitoring of microbiota and host metabolism using Secondary electrospray ionization-Mass spectrometry

The metabolic "handshake" between the microbiota and its mammalian host is a complex, dynamic process with potentially major influences on health. Dissecting the interaction between microbial species/strains and metabolites found in host tissues has been a challenge due to the high diversity of a complete micro-biota and the requirement for invasive sampling, which precludes high-resolution longitudinal analysis. Here we demonstrate that secondary electrospray ionization mass spectrometry can be used to non-invasively monitor metabolic activity of the intestinal microbiome of a live, awake mouse. This was achieved via analysis of the headspace volatile and semi-volatile metabolome of individual gut microbiota bacterial species growing in pure culture, as well as from live gnotobiotic mice specifically colonized with these microbes (i.e. metabolites released to the atmosphere via breath, the skin and from the gut). The microbial origin of these compounds was confirmed by feeding of heavy-isotope labeled microbiota-accessible sugars. This reveals that the microbiota is a major contributor to the released metabolites of a whole live mouse, and that it is possible to capture the catabolism of sugars and cross-feeding within the gut microbiota of a living animal using volatile/semi-volatile metabolite monitoring.

systems biology↗

bioRxiv2021

Circadian patterns of energy metabolism are only partially reconstituted in gnotobiotic mice

The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiome to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat-mass than germ-free or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure and respiratory quotient using a novel isolator-housed metabolic cage system which allows long-term measurements without contamination risk. This demonstrated that microbiota- released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and germ-free mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well-integrated into appetite control. We also observed no significant difference in energy expenditure per gram lean mass between the different microbiota groups, suggesting that cumulative very small differences in energy balance, or altered energy storage must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: in germ-free mice the respiratory exchange ratio was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied germ-free mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a germ-free-like drop in liver glycogen storage during the light cycle and both liver and plasma metabolomes of OligoMM12 mice clustered closely with germ-free mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle, and which are absent in the OligoMM12 consortium.

microbiology↗

bioRxiv2020

Dynamic phenotypic heterogeneity generated by delayed genetic oscillations

Eukaryotes and prokaryotes exploit the ability of genetically identical cells to exhibit different phenotypes in order to enhance their survival. However, the mechanisms by which cells transition from one phenotype to another remain unclear. Canonical models of this dynamic posit that molecular fluctuations provide the noise that drives the cell out of one stable state and into another. Stochastic processes generated by canonical models should, therefore, be good descriptors of phenotype dynamics and between-state transitions should become more likely at greater noise amplitude, for instance at higher extracellular temperatures. To test these predictions, we observed temporal expression dynamics of the promoter of a flagellum gene, fliC, in a microfluidic device using Salmonella enterica serovar Typhimurium and green fluorescent protein (GFP). Our observations show that while cells can exhibit multistable phenotypes, including stable fliC-OFF and fliC-ON states characterised by low and high GFP levels, respectively, between-state transitions can exhibit oscillatory dynamics whose return statistics do not conform to canonical theories. For example, here the fliC-ON state was more frequent following a temperature increase. To better understand our data we developed different dynamical frameworks to predict fliC expression data. We conclude that a stochastic dynamical system tailored to the genetic network of fliC is better suited to our data than prior theories where dynamical features, like oscillations and pulsing, are driven by inevitable delays in the post-translational regulation of fliC. Thus, while transcriptional noise promotes phenotypic heterogeneity, as we show here, regular features like oscillatory heterogeneity can result from delays that fundamental molecular processes impose upon a cells gene regulatory architecture.

systems biology↗

bioRxiv2019

Rationally designed oral vaccines can set an evolutionary trap for Salmonella Typhimurium

Introductory paragraphThe ability of gut bacterial pathogens to escape immunity by antigenic variation, particularly via changes to surface-exposed antigens, is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2, 3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here we demonstrated this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: A long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase-variation4, 5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen specific IgA and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of oral vaccines, we rationally induced IgA responses blocking all of these trajectories, which selected for Salmonella mutants carrying deletions of the O-antigen polymerase wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents, complement), predation (bacteriophages), and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.

immunology↗