Site-specific immobilization of the endosialidase reveals QSOX2 is a novel polysialylated protein.

Polysialic acid (polySia) is a linear polymer of α2,8-linked sialic acid residues that is of fundamental biological interest due to its pivotal roles in the regulation of the nervous, immune, and reproductive systems in healthy human adults. PolySia is also dysregulated in several chronic diseases, including cancers and mental health disorders. However, the mechanisms underpinning polySia biology in health and disease remain largely unknown. The polySia-specific hydrolase, endoneuraminidase NF (EndoN), and the catalytically inactive polySia lectin EndoNDM, have been extensively used for studying polySia. However, EndoN is heat stable and remains associated with cells after washing. When studying polySia in systems with multiple polysialylated species, the residual EndoN that cannot be removed confounds data interpretation. We developed a strategy for site-specific immobilization of EndoN on streptavidin-coated magnetic beads. We showed that immobilizing EndoN allows for effective removal of the enzyme from samples, while retaining hydrolase activity. We used the same strategy to immobilize the polySia lectin EndoNDM, which enabled the enrichment of polysialylated proteins from complex mixtures such as serum for their identification via mass spectrometry. We used this methodology to identify a novel polysialylated protein, QSOX2, which is secreted from the breast cancer cell line MCF-7. This method of site-specific immobilization can be utilized for other enzymes and lectins to yield insight into glycobiology.

Longevity of dental restorations in Sjogren's disease patients using electronic dental and health record data.

BACKGROUND: Decreased salivary secretion is not only a risk factor for carious lesions in Sjögren's disease (SD) but also an indicator of deterioration of teeth with every restorative replacement. This study determined the longevity of direct dental restorations placed in patients with SD using matched electronic dental record (EDR) and electronic health record (EHR) data. METHODS: We conducted a retrospective cohort study using EDR and EHR data of Indiana University School of Dentistry patients who have a SD diagnosis in their EHR. Treatment history of patients during 15 years with SD (cases) and their matched controls with at least one direct dental restoration were retrieved from the EDR. Descriptive statistics summarized the study population characteristics. Cox regression models with random effects analyzed differences between cases and controls for time to direct restoration failure. Further the model explored the effect of covariates such as age, sex, race, dental insurance, medical insurance, medical diagnosis, medication use, preventive dental visits per year, and the number of tooth surfaces on time to restoration failure. RESULTS: At least one completed direct restoration was present for 102 cases and 42 controls resulting in a cohort of 144 patients' EDR and EHR data. The cases were distributed as 21 positives, 57 negatives, and 24 uncertain cases based on clinical findings. The average age was 56, about 93% were females, 54% were White, 74% had no dental insurance, 61% had public medical insurance, < 1 preventive dental visit per year, 94% used medications and 93% had a medical diagnosis that potentially causes dry mouth within the overall study cohort. About 529 direct dental restorations were present in cases with SD and 140 restorations in corresponding controls. Hazard ratios of 2.99 (1.48-6.03; p = 0.002) and 3.30 (1.49-7.31, p-value: 0.003) showed significantly decreased time to restoration failure among cases and positive for SD cases compared to controls, respectively. Except for the number of tooth surfaces, no other covariates had a significant influence on the survival time. CONCLUSION: Considering the rapid failure of dental restorations, appropriate post-treatment assessment, management, and evaluation should be implemented while planning restorative dental procedures among cases with SD. Since survival time is decreased with an increase in the number of surfaces, guidelines for restorative procedures should be formulated specifically for patients with SD.

The sweet side of sex as a biological variable.

Glycobiology as a field holds enormous potential for understanding human health and disease. However, few glycobiology studies adequately address the issue of sex differences in biology, which severely limits the conclusions that can be drawn. Numerous CAZymes, lectins, and other carbohydrate-associated molecules have the potential to be differentially expressed and regulated with sex, leading to differences in O-GlcNAc, N-glycan branching, fucosylation, sialylation, and proteoglycan structure, among others. Expression of proteins involved in glycosylation is influenced through hormones, miRNA, and gene dosage effects. In this review, we discuss the benefits of incorporating sex-based analysis in glycobiology research and the potential drivers of sex differences. We highlight examples of where incorporation of sex-based analysis has led to insights into glycobiology. Finally, we offer suggestions for how to proceed moving forward, even if the experiments are already complete. Properly incorporating sex based analyses into projects will substantially improve the accuracy and reproducibility of studies as well as accelerate the rate of discovery in the glycosciences.

The cancer-associated glycan polysialic acid is dysregulated in systemic sclerosis and is associated with fibrosis.

OBJECTIVE: Systemic sclerosis (SSc) is a rare but deadly disease characterized by autoimmunity, vasculopathy, and fibrosis. Fibrotic complications associated with SSc correlate with severe morbidity and mortality. Previous studies in SSc have identified fibroblasts as the primary drivers of fibrosis; however, the mechanism(s) promoting this are not well understood. Aberrant glycosylation, particularly polysialylation (polySia), has been described as a prominent feature of aggressive cancers. Inspired by this observation, we aimed to determine if polySia is dysregulated in various forms of SSc. METHODS: All patients with SSc met the 2013 ACR/EULAR. Patients were sub-classified into limited cutaneous (lSSc, N = 5 or 46 patients for polySia quantification in the dermis or serum; respectively), diffuse cutaneous (dSSc, N = 11 or 18 patients for polySia quantification in the dermis or serum; respectively), or patients with dSSc treated with an autologous stem cell transplantation (post-ASCT, N = 4 patients for quantification in the dermis). Dermal polySia levels were measured via immunofluorescence microscopy in 10 µm dermal sections, quantified in each group (healthy volunteers (HC), lSSc, dSSc, and post-ASCT) and correlated with skin fibrosis (via the modified Rodnan skin score (mRSS)). Similarly, serum polySia was quantified in each group, and correlated with the mRSS. RESULTS: Dermal polySia levels were highest in patients with dSSc (compared to HC < 0.001), and correlated with the degree of fibrosis in all of the groups (P = 0.008). Serum polySia was higher in all SSc groups (p < 0.001) and correlated with the severity of mRSS (p < 0.0001). CONCLUSION: Polysia is more abundant in the skin and sera from patients with SSc and correlates with the degree of skin fibrosis. The aberrant expression of polySia highlights its potential use as a biomarker in patients with progressive forms of SSc. Dysregulated polySia levels in SSc further emphasizes the cancer-like phenotype present in SSc, which may promote fibrosis and immune dysregulation.

TePhe, a tellurium-containing phenylalanine mimic, allows monitoring of protein synthesis in vivo with mass cytometry.

Protein synthesis is central to maintaining cellular homeostasis and its study is critical to understanding the function and dysfunction of eukaryotic systems. Here we report L-2-tellurienylalanine (TePhe) as a noncanonical amino acid for direct measurement of protein synthesis. TePhe is synthetically accessible, nontoxic, stable under biological conditions, and the tellurium atom allows its direct detection with mass cytometry, without postexperiment labeling. TePhe labeling is competitive with phenylalanine but not other large and aromatic amino acids, demonstrating its molecular specificity as a phenylalanine mimic; labeling is also abrogated in vitro and in vivo by the protein synthesis inhibitor cycloheximide, validating TePhe as a translation reporter. In vivo, imaging mass cytometry with TePhe visualizes translation dynamics in the mouse gut, brain, and tumor. The strong performance of TePhe as a probe for protein synthesis, coupled with the operational simplicity of its use, suggests TePhe could become a broadly applied molecule for measuring translation in vitro and in vivo.

A new ELISA assay demonstrates sex differences in the concentration of serum polysialic acid.

Male and female immune systems are strikingly different and yet little is known about sex differences in immune glycans, though glycans play central roles in regulating the immune response. Polysialic acid (polySia) occurs on the majority of leukocytes and is a potent immunomodulatory glycan which enables cell migration and serves as an immune checkpoint. Due to widespread influence of polySia on the immune system, we aimed to characterize its levels in serum, its presence on specific proteins, and differences in the amounts of polySia in male and female serum. However, polySia is difficult to quantify and detect on specific proteins, which makes it challenging to elucidate the molecular details of polySia function. We developed a sandwich ELISA that allows for the quantification of polySia as well as specific polysialylated proteins in complex mixtures without any pretreatment or harsh conditions. The assay is quick, linear, and robust under a wide variety of conditions and gave a limit of detection of approximately 0.2 ng polySia per mL of serum. We then quantified polySia and polysialylated CD56 in human and mouse serum. These studies strongly support our hypothesis of differences in glycosylation between the sexes as significantly less polySia was observed in female samples than in male samples.

Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche.

Cell size and growth kinetics are fundamental cellular properties with important physiological implications. Classical studies on yeast, and recently on bacteria, have identified rules for cell size regulation in single cells, but in the more complex environment of multicellular tissues, data have been lacking. In this study, to characterize cell size and growth regulation in a multicellular context, we developed a 4D imaging pipeline and applied it to track and quantify epidermal cells over 3-4 d in Arabidopsis thaliana shoot apical meristems. We found that a cell size checkpoint is not the trigger for G2/M or cytokinesis, refuting the unexamined assumption that meristematic cells trigger cell cycle phases upon reaching a critical size. Our data also rule out models in which cells undergo G2/M at a fixed time after birth, or by adding a critical size increment between G2/M transitions. Rather, cell size regulation was intermediate between the critical size and critical increment paradigms, meaning that cell size fluctuations decay by ∼75% in one generation compared with 100% (critical size) and 50% (critical increment). Notably, this behavior was independent of local cell-cell contact topologies and of position within the tissue. Cells grew exponentially throughout the first >80% of the cell cycle, but following an asymmetrical division, the small daughter grew at a faster exponential rate than the large daughter, an observation that potentially challenges present models of growth regulation. These growth and division behaviors place strong constraints on quantitative mechanistic descriptions of the cell cycle and growth control.

Tellurium-based mass cytometry barcode for live and fixed cells.

Mass cytometry is a revolutionary technology that allows for the simultaneous quantification of >40 different biomarkers with cellular resolution. The biomarkers are detected using metal-labeled antibodies as well as small-molecule probes of cell size, viability, and biochemical status. Barcoding is an important component of sample preparation because it reduces processing time, eliminates sample-to-sample variation, discriminates cell doublets, reduces the amount of antibody needed, and conserves sample. We developed a thiol-reactive tellurium-based barcode, TeMal. TeMal is nontoxic at working concentrations, compatible with metal-labeled antibodies, and can readily be applied to live or fixed cells, making it advantageous and complementary compared to existing barcoding reagents. We have demonstrated the utility of TeMal by barcoding microscale samples in situ to facilitate analysis of cells from an automated cell culture system using mass cytometry.

Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing.

BACKGROUND: Cyanobacteria are important agents in global carbon and nitrogen cycling and hold great promise for biotechnological applications. Model organisms such as Synechocystis sp. and Synechococcus sp. have advanced our understanding of photosynthetic capacity and circadian behavior, mostly using population-level measurements in which the behavior of individuals cannot be monitored. Synechocystis sp. cells are small and divide slowly, requiring long-term experiments to track single cells. Thus, the cumulative effects of drift over long periods can cause difficulties in monitoring and quantifying cell growth and division dynamics. RESULTS: To overcome this challenge, we enhanced a microfluidic cell-culture device and developed an image analysis pipeline for robust lineage reconstruction. This allowed simultaneous tracking of many cells over multiple generations, and revealed that cells expand exponentially throughout their cell cycle. Generation times were highly correlated for sister cells, but not between mother and daughter cells. Relationships between birth size, division size, and generation time indicated that cell-size control was inconsistent with the "sizer" rule, where division timing is based on cell size, or the "timer" rule, where division occurs after a fixed time interval. Instead, single cell growth statistics were most consistent with the "adder" rule, in which division occurs after a constant increment in cell volume. Cells exposed to light-dark cycles exhibited growth and division only during the light period; dark phases pause but do not disrupt cell-cycle control. CONCLUSIONS: Our analyses revealed that the "adder" model can explain both the growth-related statistics of single Synechocystis cells and the correlation between sister cell generation times. We also observed rapid phenotypic response to light-dark transitions at the single cell level, highlighting the critical role of light in cyanobacterial cell-cycle control. Our findings suggest that by monitoring the growth kinetics of individual cells we can build testable models of circadian control of the cell cycle in cyanobacteria.

KpsC and KpsS are retaining 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferases involved in synthesis of bacterial capsules.

Capsular polysaccharides (CPSs) are high-molecular-mass cell-surface polysaccharides, that act as important virulence factors for many pathogenic bacteria. Several clinically important Gram-negative pathogens share similar systems for CPS biosynthesis and export; examples include Escherichia coli, Campylobacter jejuni, Haemophilus influenzae, Neisseria meningitidis, and Pasteurella multocida. Each CPS contains a serotype-specific repeat-unit structure, but the glycans all possess a lipid moiety at their reducing termini. In E. coli and N. meningitidis, the predominant lipid is a lysophosphatidylglycerol moiety that is attached to the repeat-unit domain of the CPS via multiple residues of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo), referred to as a poly-Kdo linker. The Kdo residues are ß-linked, suggesting that they are synthesized by retaining glycosyltransferases. To date, the only characterized Kdo transferases are the inverting enzymes that catalyze the α-linkages found in lipopolysaccharide. Here, we identify two conserved proteins from CPS assembly systems, KpsC and KpsS, as the ß-Kdo-transferases and demonstrate in vitro reconstitution of poly-Kdo linker assembly on a fluorescent phosphatidylglycerol acceptor. KpsS adds the first Kdo residue, and this reaction product is then extended by KpsC. Cross-complementation experiments demonstrate that the E. coli and N. meningitidis protein homologs are functionally conserved.

Conserved glycolipid termini in capsular polysaccharides synthesized by ATP-binding cassette transporter-dependent pathways in Gram-negative pathogens.

Bacterial capsules are surface layers made of long-chain polysaccharides. They are anchored to the outer membrane of many Gram-negative bacteria, including pathogens such as Escherichia coli, Neisseria meningitidis, Haemophilus influenzae, and Pasteurella multocida. Capsules protect pathogens from host defenses including complement-mediated killing and phagocytosis and therefore represent a major virulence factor. Capsular polysaccharides are synthesized by enzymes located in the inner (cytoplasmic) membrane and are then translocated to the cell surface. Whereas the enzymes that synthesize the polysaccharides have been studied in detail, the structure and biosynthesis of the anchoring elements have not been definitively resolved. Here we determine the structure of the glycolipid attached to the reducing terminus of the polysialic acid capsular polysaccharides from E. coli K1 and N. meningitidis group B and the heparosan-like capsular polysaccharide from E. coli K5. All possess the same unique glycolipid terminus consisting of a lyso-phosphatidylglycerol moiety with a ß-linked poly-(3-deoxy-d-manno-oct-2-ulosonic acid) (poly-Kdo) linker attached to the reducing terminus of the capsular polysaccharide.

Organotellurium scaffolds for mass cytometry reagent development.

Mass cytometry (MC) is a powerful tool for studying heterogeneous cell populations. In previous work, our laboratory has developed an MC probe for hypoxia bearing a methyl telluride mass tag. The methyl telluride was unoptimized, displaying stability and toxicity limitations. Here, we investigate three classes of organotelluriums as MC mass tags: methyl tellurides, trifluoromethyl tellurides and 2-alkyl-tellurophenes. NMR was used to compare the stability of these compounds in aqueous and organic solutions and the compounds were analysed for toxicity in Jurkat cells. The methyl tellurides were moderately stable to aerobic oxidation in organic solution under dry ambient conditions. The trifluoromethyl tellurides were stable to aerobic oxidation in organic solution but decomposed in aqueous solution. The 2-alkyl-tellurophenes proved to be stable in both organic and aqueous solutions under ambient conditions and showed limited toxicity (IC50 > 200 µM) in cell based assays. The synthetic feasibility, chemically stability, and limited toxicity of tellurophenes suggests these groups will be good choices for MC reagent development.

Site-specific enzymatic polysialylation of therapeutic proteins using bacterial enzymes.

The posttranslational modification of therapeutic proteins with terminal sialic acids is one means of improving their circulating half-life, thereby improving their efficiency. We have developed a two-step in vitro enzymatic modification of glycoproteins, which has previously only been achieved by chemical means [Gregoriadis G, Jain S, Papaioannou I, Laing P (2005) Int J Pharm 300:125-130). This two-step procedure uses the Campylobacter jejuni Cst-II α2,8-sialyltransferase to provide a primer on N-linked glycans, followed by polysialylation using the Neisseria meningitidis α2,8-polysialyltransferase. Here, we have demonstrated the ability of this system to modify three glycoproteins with varying N-linked glycan compositions: the human therapeutic proteins alpha-1-antitrypsin (A1AT) and factor IX, as well as bovine fetuin. The chain length of the polysialic acid addition was optimized by controlling reaction conditions. After demonstrating the ability of this system to modify a variety of proteins, the effect of polysialylation on the activity and serum half-life of A1AT was examined. The polysialylation of A1AT did not adversely affect its in vitro inhibition activity against human neutrophil elastase. The polysialylation of A1AT resulted in a significantly improved pharmacokinetic profile when the modified proteins were injected into CD-1 mice. Together, these results suggest that polysialylated A1AT may be useful for improved augmentation therapy for patients with a deficiency in this protein and that this modification may be applied to other therapeutic proteins.

Feasibility of Utilizing Electronic Dental Record Data and Periodontitis Case Definition to Automate Diagnosis.

Periodontitis is an irreversible disease leading to tooth loss, and 42% U.S. population suffers from periodontitis. Hence, diagnosing, monitoring, and determining its prevalence is critical to develop preventive strategies. However, a nationwide epidemiological study estimating the prevalence reported a concern about the discontinuation of such studies due to cost and ethical reasons. Therefore, this study determined the feasibility of utilizing electronic dental record (EDR) data and periodontitis case definition to automate periodontitis diagnosis. We utilized EDR data from the Indiana University School of Dentistry of 28,908 unique patients. We developed and tested a computer algorithm to diagnose periodontitis using the case definition. We found 44%, 22%, and 1% of patients with moderate, severe, and mild periodontitis, respectively. The algorithm worked with 100% sensitivity, specificity, and accuracy because of the excellent quality of the EDR data. We concluded the feasibility of providing automated periodontitis diagnosis from EDR data to conduct epidemiological studies across the US.

Including CAD/CAM dentistry in a dental school curriculum.

Shaping a clinical curriculum that is appropriate for novice dentists, is based on high-quality evidence of efficacy, yet reflects current practices is challenging. CAD/CAM units have been available to dentists since the late '80s. Recent improvements in the software, hardware and the clinical performance of available all-ceramic blocks have keyed a surge in interest. Based on a careful review of the systems available and, equally importantly, a review of the research regarding the longevity of reinforced glass ceramics, IUSD decided to add training on the use of the E4D CAD/CAM system to the curriculum. Students now receive lectures, preclinical hands-on training and clinical experience in fabricating all-ceramic restorations. At present any student who is interested in providing an all-ceramic restoration for his/her patient can do so using our CAD/CAM system. In a little less than one year our undergraduate dental students have provided 125 all-ceramic crowns to their patients. Clinical faculty have been impressed with the marginal fit and esthetics of the crowns. Finally, with students designing, milling, sintering and staining the restorations the CAD/CAM systems has reduced lab costs significantly.

Developing Automated Computer Algorithms to Track Periodontal Disease Change from Longitudinal Electronic Dental Records.

OBJECTIVE: To develop two automated computer algorithms to extract information from clinical notes, and to generate three cohorts of patients (disease improvement, disease progression, and no disease change) to track periodontal disease (PD) change over time using longitudinal electronic dental records (EDR). METHODS: We conducted a retrospective study of 28,908 patients who received a comprehensive oral evaluation between 1 January 2009, and 31 December 2014, at Indiana University School of Dentistry (IUSD) clinics. We utilized various Python libraries, such as Pandas, TensorFlow, and PyTorch, and a natural language tool kit to develop and test computer algorithms. We tested the performance through a manual review process by generating a confusion matrix. We calculated precision, recall, sensitivity, specificity, and accuracy to evaluate the performances of the algorithms. Finally, we evaluated the density of longitudinal EDR data for the following follow-up times: (1) None; (2) Up to 5 years; (3) > 5 and ≤ 10 years; and (4) >10 and ≤ 15 years. RESULTS: Thirty-four percent (n = 9954) of the study cohort had up to five years of follow-up visits, with an average of 2.78 visits with periodontal charting information. For clinician-documented diagnoses from clinical notes, 42% of patients (n = 5562) had at least two PD diagnoses to determine their disease change. In this cohort, with clinician-documented diagnoses, 72% percent of patients (n = 3919) did not have a disease status change between their first and last visits, 669 (13%) patients' disease status progressed, and 589 (11%) patients' disease improved. CONCLUSIONS: This study demonstrated the feasibility of utilizing longitudinal EDR data to track disease changes over 15 years during the observation study period. We provided detailed steps and computer algorithms to clean and preprocess the EDR data and generated three cohorts of patients. This information can now be utilized for studying clinical courses using artificial intelligence and machine learning methods.

Comparing gingivitis diagnoses by bleeding on probing (BOP) exclusively versus BOP combined with visual signs using large electronic dental records.

The major significance of the 2018 gingivitis classification criteria is utilizing a simple, objective, and reliable clinical sign, bleeding on probing score (BOP%), to diagnose gingivitis. However, studies report variations in gingivitis diagnoses with the potential to under- or over-estimating disease occurrence. This study determined the agreement between gingivitis diagnoses generated using the 2018 criteria (BOP%) versus diagnoses using BOP% and other gingival visual assessments. We conducted a retrospective study of 28,908 patients' electronic dental records (EDR) from January-2009 to December-2014, at the Indiana University School of Dentistry. Computational and natural language processing (NLP) approaches were developed to diagnose gingivitis cases from BOP% and retrieve diagnoses from clinical notes. Subsequently, we determined the agreement between BOP%-generated diagnoses and clinician-recorded diagnoses. A thirty-four percent agreement was present between BOP%-generated diagnoses and clinician-recorded diagnoses for disease status (no gingivitis/gingivitis) and a 9% agreement for the disease extent (localized/generalized gingivitis). The computational program and NLP performed excellently with 99.5% and 98% f-1 measures, respectively. Sixty-six percent of patients diagnosed with gingivitis were reclassified as having healthy gingiva based on the 2018 diagnostic classification. The results indicate potential challenges with clinicians adopting the new diagnostic criterion as they transition to using the BOP% alone and not considering the visual signs of inflammation. Periodic training and calibration could facilitate clinicians' and researchers' adoption of the 2018 diagnostic system. The informatics approaches developed could be utilized to automate diagnostic findings from EDR charting and clinical notes.

Attenuation of Polysialic Acid Biosynthesis in Cells by the Small Molecule Inhibitor 8-Keto-sialic acid.

Sialic acids are key mediators of cell function, particularly with regard to cellular interactions with the surrounding environment. Reagents that modulate the display of specific sialyl glycoforms at the cell surface would be useful biochemical tools and potentially allow for therapeutic intervention in numerous challenging chronic diseases. While multiple strategies are being explored for the control of cell surface sialosides, none that shows high selectivity between sialyltransferases or that targets a specific sialyl glycoform has yet to emerge. Here, we describe a strategy to block the formation of α2,8-linked sialic acid chains (oligo- and polysialic acid) through the use of 8-keto-sialic acid as a chain-terminating metabolic inhibitor that, if incorporated, cannot be elongated. 8-Keto-sialic acid is nontoxic at effective concentrations and serves to block polysialic acid synthesis in cancer cell lines and primary immune cells, with minimal effects on other sialyl glycoforms.

Metabolomic rearrangement controls the intrinsic microbial response to temperature changes.

Temperature is one of the key determinants of microbial behavior and survival, whose impact is typically studied under heat- or cold-shock conditions that elicit specific regulation to combat lethal stress. At intermediate temperatures, cellular growth rate varies according to the Arrhenius law of thermodynamics without stress responses, a behavior whose origins have not yet been elucidated. Using single-cell microscopy during temperature perturbations, we show that bacteria exhibit a highly conserved, gradual response to temperature upshifts with a time scale of ~1.5 doublings at the higher temperature, regardless of initial/final temperature or nutrient source. We find that this behavior is coupled to a temperature memory, which we rule out as being neither transcriptional, translational, nor membrane dependent. Instead, we demonstrate that an autocatalytic enzyme network incorporating temperature-sensitive Michaelis-Menten kinetics recapitulates all temperature-shift dynamics through metabolome rearrangement, which encodes a temperature memory and successfully predicts alterations in the upshift response observed under simple-sugar, low-nutrient conditions, and in fungi. This model also provides a mechanistic framework for both Arrhenius-dependent growth and the classical Monod Equation through temperature-dependent metabolite flux.

Assembly of gut-derived bacterial communities follows "early-bird" resource utilization dynamics.

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities cultured in vitro from human feces to uncover simple assembly rules and develop a predictive model of community composition upon addition of single nutrients from central carbon metabolism to a complex medium. Community membership was largely determined by the donor feces, whereas relative abundances were determined by the supplemental carbon source. The absolute abundance of most taxa was independent of the supplementing nutrient, due to the ability of fast-growing organisms to quickly exhaust their niche in the complex medium and then exploit and monopolize the supplemental carbon source. Relative abundances of dominant taxa could be predicted from the nutritional preferences and growth dynamics of species in isolation, and exceptions were consistent with strain-level variation in growth capabilities. Our study reveals that community assembly follows simple rules of nutrient utilization dynamics and provides a predictive framework for manipulating gut commensal communities through nutritional perturbations.