Biology subjects

Sichert, A.

Publications and source records attributed to Sichert, A..

11 recordsLinked to original sources

bioRxiv2026

Metabolic cascades drive spatial prebiotic fermentation in a defined gut consortium

Dietary fiber deficiency shifts the gut microbiota to degrade host mucus, compromising intestinal homeostasis. Mechanistically linking in vitro metabolic dynamics of fiber degradation to in vivo outcomes remains challenging due to a lack of representative model systems. Introducing spatial mucin structures to a defined Oligo-Mouse-Microbiota (OMM12) in vitro consortium allowed us to recapitulate the spatio-temporal dynamics of xylooligosaccharide (XOS) processing in gnotobiotic mice. XOS supplementation rapidly established a stable community state in vitro and in vivo across compositional, metabolic and transcriptional levels. XOS supplementation established distinct functional guilds: Bifidobacterium animalis and Blautia coccoides partitioning xylose and arabinose catabolism, whilst profiting from XOS degradation by Bacteroides caecimuris. Along the colonic axis, a spatial XOS gradient exposes Bl. coccoides's substrate preference for xylose and drives longitudinal functional adaptations. Altogether, our predictive platform proves that regional microenvironments govern prebiotic efficacy, highlighting spatial cascades as essential parameters for targeted microbiome interventions.

microbiology↗

bioRxiv2026

Widespread attraction of marine bacteria to the macroalgae-derived polysaccharide fucoidan

Fucoidan is the second most abundant polysaccharide in brown macroalgae, contributing up to 50% of the dissolved organic matter released daily from these algae into the ocean, substantially influencing the marine carbon cycle. Due to its complex chemical structure, fucoidan is highly resistant to microbial degradation and accumulates on the surface of macroalgae, where it contributes to regulating their microbiome. Here, we used a range of microfluidic assays to quantify the chemotactic and physiological responses of marine bacteria to fucoidan. Our results reveal that all the strains tested (14 out of 14) are attracted to fucoidan produced by two different species of brown macroalgae. Attraction occurred only at high fucoidan concentrations (0.1 to 1 mg/mL), such as those expected in the immediate vicinity of algal surfaces, whereas low concentrations elicited no response or modest chemorepulsion. Although fucoidan did not support bacterial growth under our experimental conditions, it did not impair the utilization of other carbon sources. Together, these findings suggest that fucoidan gradients can act as chemical cues guiding marine bacteria toward the nutrient-rich microenvironment of macroalgal surfaces, pointing to a potential ecological role of fucoidan in shaping macroalgal microbiota, bacterial behavior, and ultimately carbon cycling in the ocean.

microbiology↗

bioRxiv2026

Negative and neutral interactions are prevalent in interactions between marine chitin degraders

Bacterial chitin degradation contributes to global carbon cycling, particularly in marine environments where it is a highly abundant polysaccharide. Despite the taxonomic diversity of co-occurring chitin-degrading bacteria, the influence of individual traits on interactions between them remains poorly understood. Here, we measured key physiological traits of seven chitin degraders and investigated how these traits shape interaction outcomes and chitin degradation in pairwise cocultures. We found mainly negative and neutral interactions among degraders, contrasting with the synergistic dynamics observed with other complex polysaccharides. However, chitin degradation was not consistently diminished. These interaction types could be attributed to the limited partitioning of degradation products, alongside variations in enzyme repertoires and attachment behaviours that help some degraders to prevail over others. Further, we showed that one degrader can strongly inhibit the growth of others, even those possessing favourable physiological traits, likely due to the secretion of inhibitory compounds. These findings extend our understanding of the breadth of interactions among primary polysaccharide degraders and their implications for the degradation process. One-sentence SummaryThe physiological traits of bacteria that degrade chitin, a highly abundant biopolymer in marine environments, promote a range of neutral and negative interactions among them.

microbiology↗

bioRxiv2026

D-gluconate drives Salmonella growth during acute and chronic infection

Monosaccharides support Salmonella enterica serovar Typhimurium colonization of the gut, yet the role of their oxidized derivatives remains understudied. Sugar acids are largely diet-independent carbon sources generated by host-driven oxidative processes, but their contribution during infection - particularly that of less oxidized aldonic and uronic acids - has not been defined. Here, we systematically assess the role of sugar acids derived from D-glucose and D-galactose in S. Typhimurium SL1344 colonization. Among D-glucose-derived acids, D-gluconate accumulated to the highest levels and was the dominant substrate supporting luminal expansion in streptomycin-pretreated mice, exceeding the more oxidized acids D-glucuronate and D-glucarate. During chronic infection, D-glucose-derived sugar acids became increasingly important for pathogen persistence. Ecological niche invasion assays identified these compounds as a principal metabolic niche, whereas D-galactose-derived acids contributed minimally. Consistent with a transient, inflammation-linked nutrient niche, sugar acid utilization pathways were similarly prevalent in Escherichia coli from individuals with and without inflammatory bowel disease. Together, these findings identify D-gluconate as a key inflammation-dependent nutrient source that fuels Enterobacteriaceae expansion in the inflamed gut.

microbiology↗

bioRxiv2025

A division of labor controls the degradation of fucoidans in the ocean

Fucoidans--complex polysaccharides produced by brown algae and diatoms--contribute to long-term carbon sequestration due to their resistance to microbial degradation1,2. While individual microbes can break down portions of these polymers3-5, it remains unclear whether complete breakdown is possible in nature and, if so, by what mechanisms. Here we show that fucoidans are degraded through synergistic interactions between specialized bacteria with conserved metabolic functions. Using metabolomic analysis of a reconstructed marine consortium, we uncovered functional guilds of bacteria that target either the sulfated fucose backbone or the side-branches of rare monomers. This division of labor leads to an unexpectedly high number of positive interactions between different degraders that enhanced degradation efficiency up to 97.1%. Despite variation in fucoidan structure across different types of algae, the metabolic functions of degraders remained conserved, enabling quantitative prediction of degradation outcomes based on community composition. Our findings suggest that the environmental turnover of complex macromolecules depends not only on individual metabolic capabilities but also on ecological interactions shaped by substrate architecture. This work provides a mechanistic framework for understanding carbon cycling in the ocean and for engineering synthetic microbial consortia to degrade recalcitrant polysaccharides.

microbiology↗

bioRxiv2025

Single-cell mass accumulation reveals bacterioplankton growth rate in native seawater

AO_SCPLOWBSTRACTC_SCPLOWThe growth of marine microbial communities drives biogeochemical cycling of carbon and other elements, yet the growth rates of individual species within complex ocean ecosystems remain poorly understood. In particular, the coexistence of a large diversity of copiotrophic bacteria, which are capable of fast growth but typically remain at low abundance, has been interpreted as a feast or famine existence. Here we show that contrary to the notion of infrequent growth, Vibrio bacteria exhibited consistent growth rates in coastal ocean samples, despite representing only a small fraction of the total community. These observations were enabled by a suspended microchannel resonator (SMR), which we adapted to function as a single-cell chemostat. By maintaining a continuous supply of native seawater around each trapped cell, we prevented nutrient depletion and used the SMRs high mass precision to resolve growth rates that are otherwise undetectable. Vibrio species displayed significantly larger cell mass and faster growth than other community members across samples collected at different temporal intervals from days to years. Surprisingly, their growth was consistently limited by carbon, contrary to the expectation that heterotrophic bacteria in the euphotic zone would be limited by nitrogen and phosphorus due to competition with algae. The correlation between cell mass and growth rate of Vibrionaceae in seawater followed established growth laws derived from laboratory conditions, suggesting that growth physiology observed in pure cultures is applicable to wild bacterial populations. Overall, our findings suggest that rare species may play a disproportionately large role in the marine carbon cycle, with rapid biomass turnover driven by a combination of high growth rates balanced by intense predation.

microbiology↗

bioRxiv2025

Extracellular polymeric substance degradation shapes microbial community diversity

Competition for and exchange of nutrients play crucial roles in shaping microbial community function and dynamics. Although cross-feeding of small metabolites is known to drive carbon exchange among species, the importance of self-produced extracellular polymeric substances (EPS)-- which include proteins, polysaccharides, DNA, and humic-like substances-- remains less understood. Utilizing chitin-degrading microbial isolates and natural seawater communities, we found that 4-7% of the carbon from chitin degradation is converted into EPS, accounting for nearly a quarter of the exuded carbon. Different sources of EPS were found to select for distinct microbial communities. Through enzyme assays and untargeted metabolomics, we demonstrated that secreted enzymes degrade EPS in multiple steps that influence community diversity: larger oligomers are initially utilized by specialized degraders, while the subsequent breakdown into smaller oligomers, monosaccharides, and amino acids supports non-specialized consumers. These findings highlight the role of EPS as a significant carbon source exchanged between microbes, fueling metabolically diverse populations and enriching our understanding of carbon-mediated microbial interactions.

microbiology↗

bioRxiv2024

Selective preservation of fucose-rich oligosaccharides in the North Atlantic Ocean

The ocean has a substantial capacity to store carbon dioxide fixed via photosynthesis in dissolved organic molecules. An estimated 20% of the 660 Gt dissolved organic carbon in the ocean pool consists of structurally uncharacterized oligosaccharides, which appear to resist microbial degradation (Aluwihare et al., 1997). Current technologies lack the sensitivity and molecular resolution to identify these oligosaccharides. Here, we adapted graphitized carbon chromatography to extract and separate marine oligosaccharides for liquid chromatography high resolution mass spectrometry analysis. Using a newly-developed de novo annotation tool, we found 110 oligosaccharide structures in surface and deep ocean seawater at two distant locations in the North Atlantic Ocean. One group of the detected oligosaccharides was found only in surface seawater and consisted of larger and more abundant molecules detected by our analysis. A second group of smaller, less abundant oligosaccharides was detected in both the surface and deep ocean seawater of both sampled locations. The composition of oligosaccharides differed between the surface and deep ocean, with deep ocean samples relatively enriched in hard-to-metabolize deoxy-sugars, and xylose, amino sugars and uronic acids compared to simple hexoses. Notably the deoxy-sugar fucose constituted 35-40% of the monomers in deep-sea oligosaccharides, twice the percentage in surface ocean oligosaccharides. The ubiquity of deep ocean oligosaccharides indicates that they represent a preserved fraction of the carbohydrate pool. Their enrichment in specific monosaccharides suggests selective preservation of fucose-rich oligosaccharides in the deep ocean.

ecology↗

bioRxiv2024

Monosaccharides Drive Salmonella Gut Colonization in a Context-Dependent Manner

The carbohydrates that fuel gut colonization by S. Typhimurium are not fully known. To investigate this, we designed a quality-controlled mutant pool to probe the metabolic capabilities of this enteric pathogen. Using WISH-barcoding, we tested 35 metabolic mutants across five different mouse models, allowing us to differentiate between context-dependent and context-independent nutrient sources. Results showed that S. Typhimurium uses D-glucose, D-mannose, D-fructose, and D-galactose as context-independent carbohydrates across all models. The utilization of N-acetylglucosamine and hexuronates, on the other hand, was context-dependent. Furthermore, we showed that D-fructose is important in strain-to-strain competition between Salmonella serovars. Complementary experiments confirmed that D-glucose, D-fructose, and D-galactose are excellent niches for S. Typhimurium to exploit during colonization. Quantitative measurements revealed sufficient amounts of D-glucose and D-galactose in the murine cecum to drive S. Typhimurium colonization. Understanding these key substrates and their context-dependent use by enteric pathogens will inform the future design of probiotics and therapeutics to prevent diarrheal infections such as non-typhoidal salmonellosis.

microbiology↗

bioRxiv2022

Not digested: algal glycans move carbon dioxide into the deep-sea

Marine algae annually synthesize gigatons of glycans from carbon dioxide, exporting it within sinking particles into the deep-sea and underlying sea floor, unless those glycans are digested before by bacteria. Identifying algal glycans in the ocean remains challenging with the molecular resolution of conventional analytic techniques. Whether algal glycans are digested by heterotrophic bacteria during downward transport, before they can transfer carbon dioxide from the ocean surface into the deep-sea or the sea floor, remains unknown. In the Red Sea Shaban Deep, where at 1500 m water depth a brine basin acts as a natural sediment trap, we found its high salt and low oxygen concentration accumulated and preserved exported algal glycans for the past 2500 years. By using monoclonal antibodies specific for glycan structures, we detected fucose-containing sulfated polysaccharide, {beta}-glucan, {beta}-mannan and arabinogalactan glycans, synthesized by diatoms, coccolithophores, dinoflagellates and other algae living in the sunlit ocean. Their presence in deep-sea sediment demonstrates these algal glycans were not digested by bacteria. Instead they moved carbon dioxide from the surface ocean into the deep-sea, where it will be locked away from the atmosphere at least for the next 1000 years. Considering their global synthesis, quantity and stability against degradation during transport through the water column, algal glycans are agents for carbon sequestration. Significance statementAlgae and plants use the greenhouse gas carbon dioxide to synthesize polymeric carbohydrates, or glycans, for energy storage, structural support and as protection against invasion by microbes. Glycans provide protection, are carbon sinks and enable carbon sequestration for as long as they are not digested by bacteria or other organisms, which releases the carbon dioxide back in to the atmosphere. In this study, we show that non-digested algal glycans sink into the deep ocean and into marine sediment. Thus, glycans are more than food for animals and prebiotics for bacteria, they are also molecules that remove carbon dioxide from the atmosphere and transfer it to the deep-sea, where it can be stored for 1000 years and longer.

biochemistry↗

bioRxiv2021

Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during algal blooms

Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global nutrient cycling. When blooms collapse, organic carbon is transferred to higher trophic levels, microbial respiration or sinking in proportions that depend on the dominant mortality agent. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains an open question. Here, we characterized the consequences of viral infection on the microbiome composition and biogeochemical landscape of marine ecosystems by conducting a large-scale mesocosm experiment. Moniroting of seven induced coccolithophore blooms, which showed different degrees of viral infection, revealed that only high levels of viral infection caused significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, viral infection favored the growth of eukaryotic heterotrophs (thraustochytrids) over bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection can increase per-cell rates of extracellular carbon release by 2-4.5 fold. This happened via production of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.

microbiology↗