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Background Recent advances in high-throughput approaches for estimating co-localization of microbes, such as SAMPL-seq, allow characterization of the biogeography of the gut microbiome longitudinally and at an unprecedented scale. However, these high-dimensional data are complex and have unique noise properties. Results To address these challenges, we developed MCSPACE, a probabilistic AI method that infers, from microbiome co-localization data, spatially coherent assemblages of taxa, their dynamics over time, and their responses to perturbations. To evaluate MCSPACE’s capabilities, we generated the largest longitudinal microbiome co-localization dataset to date, profiling spatial relationships of microbes in the guts of mice subjected to serial dietary perturbations over 76 days. Analyses of these data and two existing human longitudinal datasets demonstrated superior benchmarking performance of MCSPACE over existing methods and moreover yielded insights into the spatiotemporal structuring of the gut microbiome, including identifying temporally persistent and dynamic microbial assemblages in the human gut, and shifts in assemblages in the murine gut induced by specific dietary components. Conclusions Our results highlight the utility of MCSPACE, which we make available to the community as an open-source software tool, for elucidating the dynamics of microbiome biogeography and gaining insights into the role of spatial relationships in host-microbial ecosystem function. 2aoT6Vr1TGYi1NKbTumMyT Video Abstract

Faecalibacterium prausnitzii , a major commensal bacterium in the human gut, is well known for its anti-inflammatory effects, which improve host intestinal health. Although several studies have reported that inulin, a well-known prebiotic, increases the abundance of F. prausnitzii in the intestine, the mechanism underlying this effect remains unclear. In this study, we applied liquid chromatography tandem mass spectrometry (LC-MS/MS)-based multiomics approaches to identify biological and enzymatic mechanisms of F. prausnitzii involved in the selective digestion of inulin. First, to determine the preference for dietary carbohydrates, we compared the growth of F. prausnitzii in several carbon sources and observed selective growth in inulin. In addition, an LC-MS/MS-based intracellular proteomic and metabolic profiling was performed to determine the quantitative changes in specific proteins and metabolites of F. prausnitzii when grown on inulin. Interestingly, proteomic analysis revealed that the putative proteins involved in inulin-type fructan utilization by F. prausnitzii , particularly β-fructosidase and amylosucrase were upregulated in the presence of inulin. To investigate the function of these proteins, we overexpressed bfrA and ams, genes encoding β-fructosidase and amylosucrase, respectively, in Escherichia coli, and observed their ability to degrade fructan. In addition, the enzyme activity assay demonstrated that intracellular fructan hydrolases degrade the inulin-type fructans taken up by fructan ATP-binding cassette transporters. Furthermore, we showed that the fructose uptake activity of F. prausnitzii was enhanced by the fructose phosphotransferase system transporter when inulin was used as a carbon source. Intracellular metabolomic analysis indicated that F. prausnitzii could use fructose, the product of inulin-type fructan degradation, as an energy source for inulin utilization. Taken together, this study provided molecular insights regarding the metabolism of F. prauznitzii for inulin, which stimulates the growth and activity of the beneficial bacterium in the intestine.

Tyrian purple, mainly composed of 6,6'-dibromoindigo (6BrIG), is an ancient dye extracted from sea snails and was recently demonstrated as a biocompatible semiconductor material. However, its synthesis remains limited due to uncharacterized biosynthetic pathways and the difficulty of regiospecific bromination. Here, we introduce an effective 6BrIG production strategy in Escherichia coli using tryptophan 6-halogenase SttH, tryptophanase TnaA and flavin-containing monooxygenase MaFMO. Since tryptophan halogenases are expressed in highly insoluble forms in E. coli , a flavin reductase (Fre) that regenerates FADH 2 for the halogenase reaction was used as an N-terminal soluble tag of SttH. A consecutive two-cell reaction system was designed to overproduce regiospecifically brominated precursors of 6BrIG by spatiotemporal separation of bromination and bromotryptophan degradation. These approaches led to 315.0 mg l −1 6BrIG production from tryptophan and successful synthesis of regiospecifically dihalogenated indigos. Furthermore, it was demonstrated that 6BrIG overproducing cells can be directly used as a bacterial dye. A two-cell setup containing tryptophanase, a flavin-dependent monooxygenase and a regiospecific halogenase (linked to a flavin reductase as a solubility tag) enables the production of 6,6'-dibromoindigo and other indigoid dyes in Escherichia coli .

The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or ‘spatial hubs’ dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale. Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.

Enzymes are widely used in industrial and pharmaceutical applications, but their activities often decrease rapidly under harsh environmental conditions such as heat, organic solvents, and dehydration. In this study, a new method for enzyme coating with polysaccharide using a rapid tyrosinase-mediated crosslinking reaction was developed. When tyrosinase reacts with a monophenol-containing biopolymer such as polysaccharide, it forms a covalent crosslink between the biopolymer and the enzyme. This crosslinking reaction create a rigid polysaccharide-coated enzyme (PCE) that protects the enzyme from harsh environmental conditions, that leads to improve the enzyme stability. To demonstrate the concept, trypsin (TR), a model enzyme with a positively charged surface, was used. Tyramine conjugated alginate polymer (AlgT), a negatively charged biocompatible polysaccharide, was used to coat TR. The AlgT was subsequently used to coat TR, forming an AlgT-TR complex. We characterized the PCE using particle size, surface charge (zeta potential), optimal pH shift, etc. Afterwards, we compared the enzyme kinetics of AlgT-TR and uncoated TR (free-TR). The AlgT-TR showed a higher activity and higher heat, storage, and water-miscible organic solvent stabilities than the free-TR. The AlgT coating method was efficient and effective to increase the thermal stability of not only TR, but also hydrolases with neutral to negative surface charges, such as elastase, subtilisin, and chymotrypsin. These results suggest that the tyrosinase-mediated crosslinking reaction is a very promising and general coating method for improving the stability of enzymes with positive surface charge, but the opposite case would be also possible.

Each subregion of the amygdala is characterized by a distinct cytoarchitecture and function. However, most previous studies on sexual dimorphism and aging have assessed differences in the structure of the amygdala at the level of the amygdala in its entirety rather than at the subregional level. Using an amygdala subregional shape analysis, we investigated the effects of sex, age, and the sex×age interaction on the subregion after controlling for intracranial volume. We found the main effect of age in the subregions and the effect of sex in the superficial nucleus, which showed that men had a larger mean radius than women. We also found a sex×age interaction in the centromedial nucleus, in that the radius of the centromedial nucleus showed a steeper decline with age in women compared with men. Regarding the amygdala volume as a whole, we found only an age effect and did not find any other significant difference between genders. The sex difference in the amygdala subregion and its relevance to the circulating gonadal hormone were discussed.

Recent advances in high-throughput approaches for estimating co-localization of microbes, such as SAMPL-seq, allow characterization of the biogeography of the gut microbiome longitudinally and at unprecedented scale. However, these high-dimensional data are complex and have unique noise properties. To address these challenges, we developed MCSPACE, a probabilistic AI method that infers from microbiome co-localization data spatially coherent assemblages of taxa, their dynamics over time, and their responses to perturbations. To evaluate MCSPACE's capabilities, we generated the largest longitudinal microbiome co-localization dataset to date, profiling spatial relationships of microbes in the guts of mice subjected to serial dietary perturbations over 76 days. Analyses of these data and an existing human longitudinal dataset demonstrated superior benchmarking performance of MCSPACE over existing methods, and moreover yielded insights into spatiotemporal structuring of the gut microbiome, including identifying temporally persistent and dynamic microbial assemblages in the human gut, and shifts in assemblages in the murine gut induced by specific dietary components. Our results highlight the utility of our method, which we make available to the community as an open-source software tool, for elucidating dynamics of microbiome biogeography and gaining insights into the role of spatial relationships in host-microbial ecosystem function.

The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or \"spatial hubs\" dominated by , , and families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.

Poly(3-hydroxybutyrate) is a biodegradable plastic produced by various microbes. Considering the emerging environmental problems caused by plastics, P(3HB) has gained attention as a substitute for conventional plastics. In this study, we isolated a novel P(3HB)-producing microbe, Limimaricola sp. YI8, which utilized sucrose as a cost-effective carbon source for P(3HB) production. Under optimized conditions, Limimaricola sp. YI8 produced 6.2 g/L P(3HB) using sucrose as the sole carbon source. P(3HB) extracted from YI8 exhibited a pinkish color derived from a dye produced naturally by YI8. Films fabricated from extracted P(3HB) polymer were subjected to analyses, including gel permeation chromatography, universal test machine, and differential scanning calorimetry, to determine their physical properties. The obtained values were almost identical to those of P(3HB) films extracted from Escherichia coli and Cupriavidus necator H16. Overall, this study presents the potential of Limimaricola spp. YI8 as a P(3HB)-producing strain and the P(3HB) films extracted from this strain.

Owing to recent advances in thoracic electrical impedance tomography (EIT), a patient’s hemodynamic function can be noninvasively and continuously estimated in real-time by surveilling a cardiac volume signal (CVS) associated with stroke volume and cardiac output. In clinical applications, however, a CVS is often of low quality, mainly because of the patient’s deliberate movements or inevitable motions during clinical interventions. This study aims to develop a signal quality indexing method that assesses the influence of motion artifacts on transient CVSs. The assessment is performed on each cardiac cycle to take advantage of the periodicity and regularity in cardiac volume changes. Time intervals are identified using the synchronized electrocardiography system. We apply divergent machine-learning methods, which can be sorted into discriminative-model and manifold-learning approaches. The use of machine-learning could be suitable for our real-time monitoring application that requires fast inference and automation as well as high accuracy. In the clinical environment, the proposed method can be utilized to provide immediate warnings so that clinicians can minimize confusion regarding patients’ conditions, reduce clinical resource utilization, and improve the confidence level of the monitoring system. Numerous experiments using actual EIT data validate the capability of CVSs degraded by motion artifacts to be accurately and automatically assessed in real-time by machine learning. The best model achieved an accuracy of 0.95, positive and negative predictive values of 0.96 and 0.86, sensitivity of 0.98, specificity of 0.77, and AUC of 0.96.