Microcarrier surface topography and fluid shear stress (FSS) critically regulate cellular behavior. An edible zein/fucoidan microcarrier with 200 μm grooves was designed for this study. Computational fluid dynamics (CFD) simulations and experiments were combined to analyze surface microfluidic characteristics during dynamic culture and their cellular effects. The research demonstrates controlled myogenic differentiation through groove topography and FSS modulation for scalable cultured meat production. The results demonstrated that the grooved microcarriers exhibited excellent cell attachment and proliferation capacity in spinner flask dynamic culture, achieving a maximum cell density of 1.16 × 10 cells/mL, comparable to commercial Cultispher-S microcarriers. The groove structure promoted cell alignment through contact guidance, significantly enhancing the gene expression of myogenic differentiation markers (myogenic differentiation 1, MyoD1; α-actinin; myosin heavy chain, MHC) and cell fusion (myomaker, MYMK). CFD simulations revealed that the grooves created a low-shear microenvironment (minimum average FSS: 3.93 × 10 Pa, maximum: 1.18 × 10 Pa), which effectively avoided high FSS-induced damage while maintaining mechanical stimulation. This optimal mechanical microenvironment further activated the expression of key genes involved in early-stage (MyoD1; myogenin, MyoG; myocyte enhancer factor 2C, MEF2C) and late-stage (α-actinin; myosin heavy chain 2, Myh2) myogenic differentiation. Flat and spherical microcarriers showed lower myogenic differentiation efficiency. This study elucidates the synergistic mechanism between groove structures and the low FSS microenvironment within grooves, providing a novel scaffold design rationale that combines biomimetic topology with fluid dynamics compatibility for large-scale cultured meat production.

Fermentation by microorganisms has attracted attention for the synthesis of bulk and fine chemicals with high added value, including pharmaceutical intermediates. To accelerate the development of high-producing microbial strains, a rapid screening method is warranted. This study aimed to develop a novel, nondestructive approach to quantify metabolite production in microbial colonies using hyperspectral imaging (HSI). As a model, we examined the heterologous production of 1,3,5-trihydroxyanthraquinone (AQ256), an anthraquinone with antimicrobial and anticancer activities, using Escherichia coli. Fluorescence spectral data from HSI, along with AQ256 concentrations measured via high-performance liquid chromatography, were used to construct regression models. In addition, red-green-blue (RGB)-based models were developed, as AQ256 exhibits a characteristic reddish-brown color. Four regression models were compared: multiple linear regression, partial least squares regression (PLSR), support vector regression, and random forest regression. Among them, the PLSR model based on HSI data showed the highest prediction accuracy (R = 0.75 ± 0.23, root mean square error = 0.08 ± 0.02, mean absolute error = 0.07 ± 0.02). In particular, it outperformed the RGB-based model in extrapolation beyond the training data. These findings demonstrate that the HSI-based method enables accurate, nondestructive quantification of metabolites and has strong potential for high-throughput screening of microbial strains that produce various valuable compounds at elevated yields.

Dendritic cells (DCs) are professional antigen-presenting cells that play a central role in initiating and shaping adaptive immune responses. Targeting antigens to DCs has emerged as a promising strategy to enhance vaccine efficacy and tailor desired immune responses. While antibodies are well established as targeting molecules for DCs, the use of peptides remains underexplored despite their favorable tissue penetration and their ability to offer design flexibility. Here, we report the identification of dectin-1-binding peptides using a ribosome display-based in vitro directed evolution system. Dectin-1 is a C-type lectin receptor expressed on murine CD11b and human CD1c DCs, which plays a key role in antigen uptake and in directing immune responses toward specific pathways, particularly the Th17 pathway. Using recombinant murine dectin-1 as bait, we performed four rounds of ribosome display selection and obtained peptides with high affinity. Selected peptides fused to enhanced green fluorescent protein showed binding to recombinant dectin-1 and native dectin-1-expressing cells, including bone marrow-derived DCs. These results demonstrated the feasibility of peptide-based molecular targeting toward dectin-1 DCs, which would not only provide a versatile platform for the development of next-generation vaccines and immunotherapies, but also a valuable tool for dissecting the functional roles of dectin-1 DCs in immune regulation.

Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.

A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as Aspergillus oryzae. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in A. oryzae AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200-700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.

Aspergillus oryzae is used for brewing, and many strains with different brewing characteristics have been isolated. We compared enzymatic activities of eight A. oryzae strains, RIB40, 128, 143, 163, 301, 915, 1108, and 1178 strains, toward plant polysaccharides. The plant polysaccharide degradation-related enzymes produced by A. oryzae change depending on the monosaccharides and polysaccharides added to the culture medium. RIB915 produced more cellulolytic and hemicellulolytic enzymes, whereas RIB40, 128, and 301 produced less of these enzymes than the other strains. In addition, A. oryzae RIB128 produced different glycoside hydrolases in response to monosaccharides and polysaccharides compared with other strains. These results indicated that there is diversity in the production of plant polysaccharide degradation-related enzymes within A. oryzae species.

Pseudonocardia sp. D17 (D17) is a novel strain capable of aerobically metabolizing cis-1,2-dichloroethene (cDCE), a persistent contaminant in soil and groundwater. This study aimed to investigate the cDCE degradation characteristics of D17 with respect to kinetics, associated degradative enzymes, and degradation pathways. Degradation experiments with cDCE concentrations ranging from 0.267 to 91.3 μM revealed that D17 can efficiently degrade cDCE across this range. The maximum specific degradation rate and half saturation constant for cDCE degradation by D17 were estimated to be 0.418 ± 0.045 nmol/mg-protein/min and 38.5 ± 9.2 μM, respectively. Heterologous expression experiments demonstrated that both group 5 soluble di-iron monooxygenases in D17, namely tetrahydrofuran and propane monooxygenases, can catalyze cDCE degradation with higher catalytic activity observed in the former. This suggests their involvement in cDCE degradation by D17. It was also proposed that D17 completely dechlorinates cDCE through multiple pathways to generate glyoxylic acid, which is either mineralized or incorporated into the glyoxylate cycle, with a minor portion being converted to oxalic acid as a dead-end product. These findings provide novel insights into metabolic aerobic cDCE biodegradation and highlight the potential of D17 as a bioremediation agent.

Sake yeast exhibits remarkable fermentative capacity in mash environments, even under various stress conditions. Although breeding techniques aimed at improving the flavor of sake by modifying aroma compounds and organic acid composition have been employed, these approaches often result in reduced fermentative capacity. Furthermore, existing breeding methods aimed at enhancing fermentative capacity often result in increased acidity in the final product. In this study, we aimed to improve sake yeast fermentative capacity while limiting sake acidity. Depletion of intracellular ATP may enhance fermentative capacity, suggesting that strains with high vacuolar-type ATPase (V-ATPase) activity exhibit improved fermentative capacity. Thus, we subjected sake yeast to ultraviolet mutagenesis and bafilomycin A1 (Baf), a V-ATPase inhibitor, to select resistant strains. The selected Baf-resistant strains exhibited no changes in growth rate, cell morphology, or vacuolar morphology compared to the parent strain. However, increased vacuolar acidity and decreased intracellular ATP levels indicated enhanced V-ATPase activity. Moreover, evaluation of brewing characteristics confirmed improved fermentative capacity without increases in acidity or amino acid content. The results of this study suggest that obtaining a Baf-resistant strain can reduce intracellular ATP levels, thereby increasing fermentative capacity without increasing acidity.

A novel two-enzyme cascade one-pot synthesis of β-alanine from 1,3-diaminopropane (DAP) has been developed. In the first step, DAP was oxidized to 3-aminopropionaldehyde (3-APAL) by diamine oxidase (DAO). In the second step, 3-APAL was oxidized to β-alanine by 3-APAL dehydrogenase (APALDH). Catalase and NADH oxidase were employed to degrade the by-product, HO, and to regenerate the cofactor, NAD. DAO specific to DAP has not been reported in any prokaryote. Therefore, initial proof of concept was established using commercial eukaryotic DAO (from porcine kidney) and catalase (from bovine liver), along with recombinant APALDH and NOX enzymes sourced from Arthrobacter crystallopoietes and Lactococcus lactis, respectively. β-Alanine was successfully produced via this pathway; 12.2 mM (1.1 g/L) was formed in 41 h with 12 % conversion. To increase the reaction rate, DAO with higher specific activity was identified from Arthrobacter pascens (DAO). The optimum pH and temperature of DAO were determined to be 9.0 and 37 °C, respectively. Batch enzymatic biotransformation achieved 6 % conversion, yielding 0.33 mM (29 mg/L) β-alanine in 4 h. The low titre in batch conversion was attributed to substrate inhibition affecting DAO, NOX, and catalase. Fed-batch enzymatic biotransformation was conducted to overcome substrate inhibition, yielding 47 % conversion, with 2.34 mM (63 mg/L) β-alanine formation in 4 h. Approximately a 7.5-fold increase in conversion was achieved using fed-batch enzymatic biotransformation. This study accomplished a novel two-enzyme cascade biotransformation strategy for one-pot β-alanine synthesis from DAP.

The understanding of white-rot fungi (WRF) and their role in degrading recalcitrant environmental pollutants has significantly advanced due to developments in bioremediation research. Considerable progress has been made in elucidating the degradation capabilities of WRF against lots of environmental pollutants. In this review, research hotspots on the degradation of WRF were identified through bibliometric analysis. Key findings from systematic studies on the degradation of polycyclic aromatic hydrocarbons (PAHs) and bisphenols by WRF are synthesized and discussed. Furthermore, insights into the molecular and genetic basis underlying the enzymatic systems responsible for the degradation of PAHs and bisphenols are highlighted. Advancements and challenges in understanding the degradation capabilities and degradation mechanisms are examined in order to identify opportunities for developing more effective strategies to harness the bioremediation potential of WRF.

In this study, Pseudomonas sp. NGC7 was engineered to selectively produce vanillate (VA) from aromatic compounds in the sugarcane bagasse alkaline extract. A VA O-demethylase gene (vanA4B4)-disrupted strain derived from NGC7 grew and produced VA from the extract containing no saccharides. The organic acids in the extract promoted the strain to grow. The aromatics in the extract were further concentrated by the solid phase extraction with DIAION HP20 resin, and the organic acids were fractionated into the flow-through fraction. A fed-batch culture of NGC7ΔvanA4B4 strain using this concentrated alkaline extract exhibited increased VA production; however, the accumulation of syringate (SA) and 4-hydroxybenzoate (HBA) was also observed along with VA production, despite the strain possessing the genes responsible for SA and HBA degradation. Analysis of the mutants capable of degrading SA while producing VA revealed that mutations in vanR2, a transcriptional repressor of the genes responsible for SA degradation, enabled SA degradation during VA production. In addition, the expression of praI, an HBA hydroxylase derived from Paenibacillus sp. JJ-1b, was suitable for efficient HBA degradation. Thus, the mutation in vanR2 and the expression of praI represented the key engineering strategies for achieving the selective VA production. As the growth of the engineered strains was promoted by the organic acids present in the extract, VA production from the concentrated extract was evaluated in a flow-through-based medium supplemented with mineral salts and metals. Finally, the engineered VA-producing strain produced 4.30 mM VA selectively at a yield of 77 mol% in the practical medium.

1-(β-d-Ribofuranosyl)-1,2,4-triazole (RTA) is a nucleotide analog of 1,2,4-triazole that demonstrates broad-spectrum antiviral activity. It is currently the approved drug for treating chronic hepatitis E virus (HEV) infections. However, the production of RTA relies predominantly on chemical synthesis and extraction from plants and animals, with no report of microbial metabolic production. This study introduces a novel approach to producing RTA via solid-state fermentation (SSF) using Purpureocillium lavendulum DQWM-G4, with rice as the substrate. The chemical structure of RTA was elucidated through H and C nuclear magnetic resonance (NMR) spectroscopy. Fermentation conditions for producing RTA were optimized by investigating substrate type, temperature, and duration. Under optimized conditions, SSF with P. lavendulum DQWM-G4 on rice at 20 °C for 60 d yielded RTA at a high concentration of 3.46 ± 0.16 mg/g. This paper represents the first report on microbial production of RTA, offering an alternative to chemical synthesis and natural extraction.

Tissue engineering of thick hepatic tissues is limited by an inadequate oxygen supply, which causes hypoxia and cell death. Oxygen-generating materials have emerged to temporarily relieve hypoxia. However, quantitative analysis of their ability to generate oxygen is still lacking, hindering the precise evaluation of their efficacy. In this study, we developed an oxygen-generating collagen gel (oxy CG) containing calcium peroxide (CaO) and quantitatively analyzed its oxygen release dynamics by measuring the oxygen generation rate and calculating its volumetric oxygen transfer coefficient (ka). Using this method, we derived a theoretical threshold for cultivable cell density that was experimentally validated under hypoxic conditions using primary rat hepatocytes (PRHs). Oxy CG sustained oxygen release, while maintaining pH stability, supporting hepatocyte viability and liver-specific functions, such as urea synthesis and albumin secretion, within the predicted cell density range. This study provides a quantitative framework that balances oxygen supply and cellular demand, providing valuable insights for optimizing oxygen delivery in liver tissue engineering to overcome diffusion limitations in 3D constructs and improve clinical applicability.

Water-surface floating microalgae have a potential to be promising host organisms to produce useful compounds free from energy-consuming and costly harvesting processes. However, only a few water-surface floating microalgae have been studied for biotechnological applications. In this study, we investigated the potential of a chrysophycean alga Chromophyton sp., also known as Hikarimo in Japan, as a producer of fucoxanthin. The cells of this microalga float on the surface of freshwater in natural environments and can be harvested by attaching plastic film to the floating cells. Three strains, SH01, SH02, and SH03, were isolated from Japanese freshwater environments in Ibaraki, Nagano, and Chiba, and all three strains were identified as Chromophyton sp. by molecular phylogenetic analysis. After we prepared a less contaminated culture of these strains, culture conditions, namely medium concentrations, temperatures, and photon flux densities, were optimized to enhance the cell concentrations. As a result, the cell concentration of Chromophyton sp. reached 16.7 × 10 cells/ml, which is 10.7 times higher than that before the investigation. The cultured cells did not show a water-surface floating phenotype, and thus, we should identify the trigger(s) to induce this floating phenotype. High-performance liquid chromatography analyses revealed that Chromophyton sp. was rich in fucoxanthin. The fucoxanthin content and productivity were estimated to be 48.7 mg/g of dry cell weight and 2.31 mg/L/day, respectively. This is the highest level among the microalgal species studied so far. Since Chromophyton sp. was observed to be free from a cell wall, this microalga would also be favorable for food and feed applications.

The natural abundances of stable isotopes were used to determine prey-predator relationships and material flows in a biological treatment reactor for municipal wastewater. The reactor used in this study was a down-flow hanging sponge (DHS), which is an alternative trickling filter that uses sponge as the packing material. The sponge retained sludge containing a wide variety of organisms, including microfauna. Stable isotope analysis revealed spatial, temporal, and biotic variations in the carbon and nitrogen stable isotope ratios (δC and δN) of the retained sludge and microfauna (water mites and fly larvae). In addition, adult flies and spiders were present and analyzed. The δC and δN in sludge were temporally and spatially similar along the reactor. The isotopic signature was associated with treatment characteristics such as a low nitrification efficiency in the DHS reactor. The δC and δN of sympatric fly larvae differed from those of water mites, which indicated dietary differences between the taxa. Interestingly, the water mites had higher δC and δN than the retained sludge, which indicated that they were in a higher trophic position in the food web. In addition, the δC and δN values of spiders were approximately 1 ‰-3‰ higher than those of adult flies. This strongly suggested that a prey-predator relationship existed between adult flies and spiders.

Lipids are one of the three major nutrients that play important roles as sources of energy and as components of cell membranes. Fatty acid metabolites exhibit physiological activities. Among fatty acid metabolites, some hydroxy arachidonic acids (ARAs) have bioactive functions. In this study, we found that Torula dematia NBRC 6213 converts ARA into unknown fatty acids. Liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry, and nuclear magnetic resonance (NMR) analyses were conducted to identify this unknown fatty acid. The unknown fatty acid was identified as 14,15,19-trihydroxyeicosa-5,8,11-trienoic acid. Its production was maximized when T. dematia was cultivated in potato dextrose broth (PDB) medium and reacted for 12 h at pH 7.0 and 28 °C. In addition, multiple intermediates were formed during the conversion of ARA to 14,15,19-trihydroxyeicosa-5,8,11-trienoic acid. LC-MS analysis revealed molecular weights of 320, 336, and 338. This suggests that ARA conversion occurs via the hydroxylation, epoxidation, and hydrolysis of the epoxy group. T. dematia also converts other unsaturated fatty acids into similarly oxidized fatty acids.

Chitinases play an important role in many biological processes, including molting, digestion, and immunity in crustaceans. This study represents an attempt to apply chitinases in the field of biotechnology, detecting chitinase mRNAs from a land crab, Chiromantes haematocheir, via transcriptome analysis and analyzing their properties. Seven chitinase genes were detected from the RNA-seq data of midgut glands. Among these genes, TRINITY_DN29294 transcripts accounted for virtually all of total expression of the chitinases. The 29294 cDNA contained a 1467 bp open reading frame, coded for 488 amino acid residues, and was classified into the GH18 chitolectin chitotriosidase and the group 3 crab chitinase. The expression of the 29294-chitinase mRNA was detected in all tissues, with the highest levels expressed in the midgut glands. The transcripts increased significantly in the early post-molted crab compared to the non-molting crab. These results suggest that 29294-chitinase plays important roles in the molting process. While the recombinant 29294-chitinase over-produced in Escherichia coli did not show any activity, the enzyme expressed in Pichia pastoris exhibited sufficient activity. The 29294-chitinase had its optimal pH 3.0. The optimal temperature was relatively high at 45 °C. The enzyme hydrolyzed both soluble and crystalline substrates.

In this work, two types of Staphylococcus epidermidis fermentation broth were prepared in beef-protein medium and beef-protein medium with glucose, named as SFB and Glu-SFB. As a positive control, 0.5 mg/mL kojic acid was utilized, which led to a 33.1 ± 1.32 % drop in melanin content and a 30.9 ± 2.95 % reduction in tyrosinase activity in B16-F10 cells. After treatment with SFB and Glu-SFB, the intracellular melanin content diminished by 35.4 ± 0.67 % and 48.5 ± 1.36 %, while tyrosinase activity declined by 59.1 ± 1.49 % and 64.4 ± 2.03 %, respectively. The two S. epidermidis fermentation broth markedly diminish intracellular melanin concentrations and tyrosinase activity, leading to a whitening effect. The whitening efficacy of Glu-SFB surpasses that of SFB and exceeds that of 0.5 mg/mL kojic acid. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with untargeted metabolomics analysis was utilized to identify differential metabolites. Six oligopeptides were identified as Trp-Phe-Tyr-Leu (WFYL), Gln-Ile-Gly-Pro (QIGP), Val-Arg-Phe-Ile (VRFI), Tyr-Ile-Arg (YIR), Glu-Gln-Ile-Trp (EQIW), and His-Gly-Tyr-Lys (HGYK), exhibiting greater relative abundance in Glu-SFB than in SFB. At a dosage of 0.1 mg/mL, oligopeptide exhibits a greater capacity to diminish intracellular melanin levels and tyrosinase activity compared to 0.5 mg/mL kojic acid. Gly-SFB is prepared by replacing glucose with glycerol, the relative concentration of oligopeptides in Gly-SFB is positioned between that of SFB and Glu-SFB, while its whitening efficacy is similarly intermediate between SFB and Glu-SFB. Western blot research shown that all the S. epidermidis fermentation broths may suppress the expression of tyrosinase (TYR), tyrosinase-related protein-1 (TRP-1), tyrosinase-related protein-2 (TRP-2), and microphthalmia-associated transcription factor (MITF), which is the primary mechanism underlying the whitening impact of these broths.

The biological treatment of selenium-containing wastewater has attracted attention as a cost-effective and eco-friendly technology. However, the inhibitory effect of high salinity and oxygen in wastewater on bacterial selenate/selenite-reducing abilities hinders their practical use. In this study, a unique halotolerant facultative anaerobe, Citrobacter koseri Y2, which can reduce selenate under both aerobic and anaerobic conditions, was isolated and characterized, including a whole genome analysis. Strain Y2 reduced 1 mM selenate and selenite, and 0.4 mM selenate and 1 mM selenite to elemental selenium within 4 d at 3 % (w/v) NaCl under aerobic and anaerobic conditions. Regarding the mechanisms underlying selenate reduction, genes for selenate reductases, YnfE and YnfF, and nitrate reductases were identified in the genome of strain Y2. Selenate reduction by strain Y2 was inhibited in the presence of tungstate, confirming the involvement of molybdoenzymes in this process. These results indicate that strain Y2 is a promising bioagent for the treatment of selenium-containing wastewater.

In regenerative medicine, it is crucial to discover the key factors associated with erythroid differentiation for efficient production of artificial red blood cells. One such factor is erythroid metabolism as erythroid cells dynamically coordinate their metabolic processes to obtain energy for proper differentiation. However, the details of these metabolic changes are not well understood. In this study, we aimed to analyze the metabolism of K562, a cell line that differentiates into erythroid cells using C-metabolic flux analysis. The results showed that differentiated cells decreased glycolytic flux and increased TCA cycle flux compared with undifferentiated cells, indicating a shift to oxidative metabolism via differentiation. Based on the finding, the inhibition of ATP synthase by oligomycin treatment significantly suppressed differentiation of K562 cells, suggesting that the activation of oxidative metabolism is required for proper differentiation of K562 cells.

Cellular innate fluorescence (IF) is a natural fluorescence derived from cellular metabolites and biomolecules within microbial cells. Although IF is suggested to be a promising tool for probing the physiology of cells in a non-invasive manner, the link between single-cell IF and heterogeneity in material production remains largely unexplored. This study aimed to examine the link between cellular IF in oleaginous yeasts and their lipid-producing capabilities at multiple taxonomic levels: intra-species, inter-species, and inter-genus. Briefly, we developed a novel microscopic method that can directly link cellular IF (a single-cell IF signature) and the lipid-producing capability of cells at single-cell resolution, thereby enabling the recognition of high heterogeneity in single-cell IF and lipid production in cells. At the intra-species level, the time-course analysis revealed a parallelism between the shifts in single-cell IF signatures and lipid production by Lipomyces starkeyi. The regression model constructed based on single-cell IF signatures could predict intracellular lipid contents. The link between IF and lipid production was also observed across the inter-strain, inter-species, and inter-genus levels, where the regression model constructed with single-cell IF signatures of different strains, species, and genera could predict lipid production. Machine learning models established a computational link to predict lipid productivity by relying on the single-cell IF signatures. These results indicate that the single-cell IF signature is a promising tool for lipid production analysis and prediction in oleaginous yeast species across taxa.