Metabolic Engineering of Escherichia coli for de Novo Production of Betaxanthins

Betalains are emerging natural pigments with high tinctorial strength and stability, physiological activities, and fluorescent properties for potential application in food, cosmetic, and pharmaceutical industries. Betalains including yellow betaxanthins and red betacyanins are mainly restricted in the Caryophyllales plants. To expand the availability of individual betaxanthins, here, we constructed an Escherichia coli BTA6 for de novo biosynthesis of betalamic acid. Using this strain as a monoculture platform, 14 yellow and 2 red betaxanthins were produced by feeding amino acids and amines. Furthermore, we constructed an l-histidine overproducing strain using chromosome engineering to deattenuate regulation and established a coculture system. After optimization of the initial inoculation ratios and fermentation conditions, the compatible and robust coculture system produced 287.69 mg/L of histidine-betaxanthin. This is the first report on de novo production of betaxanthins in engineered E. coli using glucose as a carbon source. Our work highlights the feasibility of microbial cell factories to produce individual betalains.

Uveal Melanoma Cells Elicit Retinal Pericyte Phenotypical and Biochemical Changes in an in Vitro Model of Coculture

Vascular pericytes are an important cellular component in the tumor microenvironment, however, their role in supporting cancer invasion is poorly understood. We hypothesized that PDGF-BB could be involved in the transition of human retinal pericytes (HRPC) in cancer-activated fibroblasts (CAF), induced by the 92.1 uveal melanoma (UM) cell line. In our model system, HRPC were conditioned by co-culturing with 92.1UM for 6 days (cHRPC), in the presence or absence of imatinib, to block PDGF receptor-β (PDGFRβ). The effects of the treatments were tested by wound healing assay, proliferation assay, RT-PCR, high-content screening, Western blot analysis, and invasion assay. Results showed profound changes in cHRPC shape, with increased proliferation and motility, reduction of NG2 and increase of TGF-β1, α-SMA, vimentin, and FSP-1 protein levels, modulation of PDGF isoform mRNA levels, phospho-PDGFRβ, and PDGFRβ, as well as phospho-STAT3 increases. A reduction of IL-1β and IFNγ and an increase in TNFα, IL10, and TGF-β1, CXCL11, CCL18, and VEGF mRNA in cHRPC were found. Imatinib was effective in preventing all the 92.1UM-induced changes. Moreover, cHRPC elicited a significant increase of 92.1UM cell invasion and active MMP9 protein levels. Our data suggest that retinal microvascular pericytes could promote 92.1UM growth through the acquisition of the CAF phenotype.

Optimizing an Osteosarcoma-Fibroblast Coculture Model to Study Antitumoral Activity of Magnesium-Based Biomaterials

Osteosarcoma is among the most common cancers in young patients and is responsible for one-tenth of all cancer-related deaths in children. Surgery often leads to bone defects in excised tissue, while residual cancer cells may remain. Degradable magnesium alloys get increasing attention as orthopedic implants, and some studies have reported potential antitumor activity. However, most of the studies do not take the complex interaction between malignant cells and their surrounding stroma into account. Here, we applied a coculture model consisting of green fluorescent osteosarcoma cells and red fluorescent fibroblasts on extruded Mg and Mg-6Ag with a tailored degradation rate. In contrast to non-degrading Ti-based material, both Mg-based materials reduced relative tumor cell numbers. Comparing the influence of the material on a sparse and dense coculture, relative cell numbers were found to be statistically different, thus relevant, while magnesium alloy degradations were observed as cell density-independent. We concluded that the sparse coculture model is a suitable mechanistic system to further study the antitumor effects of Mg-based material.

Aging affects responsiveness of peripheral blood mononuclear cells to immunosuppression of periodontal ligament stem cells

Objectives

The effect of age on the response of peripheral blood mononuclear cells (PBMCs) to immunosuppression induced by human periodontal ligament stem cells (hPDLSCs) is unclear. The identity of the cytokines most effective in inducing the PBMC immune response remains unknown. This study investigated the effects of age on immunophenotype, proliferation, activation, and cytokine secretion capacities of PBMCs following co-culture with hPDLSCs.

Methods

PBMCs were collected from younger (16–19 years) and older (45–55 years) donors, then co-cultured with confirmed hPDLSCs for various lengths of time. T lymphocyte proliferation and cell surface marker expression were analyzed by flow cytometry. Cytokine expression levels were measured by quantitative polymerase chain reaction assays and enzyme-linked immunosorbent assays.

Results

CD28 expression by T lymphocytes decreased with age, indicating reduced proliferation; CD95 expression increased with age, indicating enhanced apoptosis. Moreover, hPDLSCs inhibited T lymphocyte proliferation in both age groups; this inhibition was stronger in cells from older donors than in cells from younger donors. Age reduced the secretion of interleukin-2 and interferon-γ, whereas it increased the secretion of tumor necrosis factor-β by PBMCs cultured with hPDLSCs.

Conclusions

Aging may have a robust effect on the response of PBMCs towards hPDLSC-induced immunosuppression.

Enhanced chondrogenesis in a coculture system with genetically manipulated dedifferentiated chondrocytes and ATDC5 cells

Articular cartilage repair after injury is a great challenge worldwide due to its nerveless and avascular features. Tissue engineering is proposed as a promising alternative for cartilage regeneration. In this study, an adenoviral vector carrying the transforming growth factor-β3 (TGF-β3) gene was constructed and introduced into dedifferentiated chondrocytes, which were then cocultured with ATDC5 cells in an alginate hydrogel system. The results showed that the experimental groups exhibited better cell viability and higher levels of cartilage-related genes than the control groups. In this coculture system, the chondrogenic differentiation of ATDC5 cells was effectively induced by TGF-β3 and other latent cytokines that were produced by the transfected chondrocytes. Thus, this method can avoid the degradation of exogenous TGF-β3, and it can protect ATDC5 cells during virus transfection to maintain cell viability and chondrogenic differentiation capability. Taken together, this study provides fresh insights for applying this genetically manipulated coculture system to cartilage repair in the future.

Prostate cancer cells modulate the differentiation of THP-1 cells in response to etoposide and TLR agonists treatments

The aim of this study was to determine the polarization of macrophages in the tumor microenvironment, as well as the effect of soluble factors secreted from these polarized macrophages on etoposide-induced cancer cell apoptosis. We investigated the effect of soluble factors secreted from the supernatant of PC3 cells treated with TLR4 and TLR8 agonists, and etoposide on macrophage polarization at the protein level through flow cytometry and enzyme-linked immunosorbent assay. We further explored the cell cycle distribution and phagocytic activity of THP-1 cells by flow cytometry. To imitate the relationship between cancer cells and tumor-associated macrophages (TAMs), we cocultured macrophages with etoposide-treated PC3 cells. After the incubation, the apoptosis in cancer cells was assessed through FACS analysis and by annexin V and PI staining. Our results demonstrate that protein expression of M1 and M2 markers confirmed the upregulation of M1 markers upon etoposide treatment, and mixed M1/M2 phenotype upon treatment with TLR agonists-treated PC3 supernatant. In coculture methods, our results demonstrate that the apoptosis of etoposide-treated cancer cells increases in the presence of M0 macrophages and THP-1 cells incubated with the supernatant of TLR4 agonists-treated PC3 cells. These results indicate clear protective effects of M0 macrophages and THP-1 cells incubated with the supernatant of PC3 cells treated with TLR4 agonists (THP-1 + SUP +  TLR4a) on etoposide-induced cancer cell apoptosis.

Modulation of Mammalian Cardiomyocyte Cytokinesis by the Extracellular Matrix

RATIONALE

After birth, cycling mammalian CMs (cardiomyocytes) progressively lose the ability to undergo cytokinesis and hence they become binucleated, which leads to cell cycle exit and loss of regenerative capacity. During late embryonic and early postnatal heart growth, CM development is accompanied by an expansion of the cardiac fibroblast (cFb) population and compositional changes in the ECM (extracellular matrix). Whether and how these changes influence cardiomyocyte cytokinesis is currently unknown.

OBJECTIVE

To elucidate the role of postnatal cFbs and the ECM in cardiomyocyte cytokinesis and identify ECM proteins that promote cardiomyocyte cytokinesis.

METHODS AND RESULTS

Using primary rat cardiomyocyte cultures, we found that a proportion of postnatal, but not embryonic, cycling cardiomyocytes fail to progress through cytokinesis and subsequently binucleate, consistent with published reports of in vitro and in vivo observations. Direct coculture with postnatal cFbs increased cardiomyocyte binucleation, which could be inhibited by RGD peptide treatment. In contrast, cFb-conditioned medium or transwell coculture did not significantly increase cardiomyocyte binucleation, suggesting that cFbs inhibit cardiomyocyte cytokinesis through ECM modulation rather than by secreting diffusible factors. Furthermore, we found that both embryonic and postnatal CMs binucleate at a significantly higher rate when cultured on postnatal cFb-derived ECM compared with embryonic cFb-derived ECM. These cytokinetic defects correlate with cardiomyocyte inefficiency in mitotic rounding, a process which is key to successful cytokinesis. To identify ECM proteins that modulate cardiomyocyte cytokinesis, we compared the composition of embryonic and postnatal cFb-derived ECM by mass spectrometry followed by functional assessment. We found that 2 embryonically enriched ECM proteins, SLIT2 and NPNT (nephronectin), promote cytokinesis of postnatal CMs in vitro and in vivo.

CONCLUSIONS

We identified the postnatal cardiac ECM as a nonpermissive environment for cardiomyocyte cytokinesis and uncovered novel functions for the embryonic ECM proteins SLIT2 and NPNT (nephronectin) in promoting postnatal cardiomyocyte cytokinesis. Graphic Abstract: A graphic abstract is available for this article.

Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism

Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N₂ gas and provides nitrogen to E. coli in the form of NH₄ ⁺ The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. In addition, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a priori IMPORTANCE Microbial communities impact life on Earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodopseudomonas palustris Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.

DNA Stability, Regeneration Capacity, and Mucociliary Differentiation of Human Nasal Mucosa Cells in Tissue Systems

For culture models of primary cells of the human nasal mucosa, monocultures with epithelial cells (ECs) are used as well as cocultures with ECs and fibroblasts (FBs). Well-differentiated models of the respiratory nasal epithelium can be used for ecogenotoxicological assessments, for experiments on host/pathogen interactions, or tissue engineering. However, long-term cultivation and repeated passaging may induce a loss of DNA integrity or cell functionality. The aim of this study was to evaluate these parameters in test systems created from primary nasal mucosa cells. Enzymatic and sequential cell isolation from nasal tissue was performed. EC monocultures and compartment-separated EC-FB cocultures were cultivated over three passages under air/liquid interface conditions. DNA stability and regenerative capacity at the DNA and chromosomal level as well as proliferation and cell differentiation were examined. Both methods showed equivalent levels of DNA stability and regenerative capacity over all passages. Sequential growth of the coculture provided higher cell purity, while enzymatic cell harvest was associated with FB contamination in EC culture. Mucociliary differentiation was verified with electron microscopy in both methods. Functionality measured by lipopolysaccharide stimulation of interleukins was constant over long-term cultivation. Our data confirm DNA stability in long-term cell cultivation as well as functional integrity in both culture methods. Sequential cell isolation should be favored over enzymatic isolation due to higher culture purity. Impact statement Cell culture models are frequently used for ecogenotoxicological assessments, for experiments on host/pathogen interactions, or tissue engineering. However, DNA stability and functional integrity after long-term cultivation in such tissue models have not been investigated, yet. This study is the first showing systematic and evident data on DNA damage and functional aspects in primary human cell culture models of nasal epithelium.

Human Menstrual Blood-Derived Mesenchymal Cells Improve Mouse Embryonic Development

There is a constant need for improving embryo culture conditions in assisted reproduction. One possibility is to use mesenchymal stem/stromal cells derived from menstrual blood (mbMSCs), with an endometrial origin. In this study, we sought to analyze the expansion of mouse embryos in a direct coculture model with mbMSCs. Our results showed that after five passages, mbMSCs presented a spindle-shaped morphology, with surface markers that were comparable with the normal mesenchymal cell phenotype. mbMSCs could differentiate into adipogenic and osteogenic lineages and secrete angiopoetin-2 and hepatocyte growth factor. The coculture experiments employed 103 two-cell-stage embryos that were randomly divided into two groups: control (n = 50), embryos cultured in GV-Blast medium, and cocultured mbMSCs (n = 53), embryos cocultured with GV-Blast and mbMSCs. Typically, two to three embryos were placed in a well with 200 μL of culture medium and observed until developmental day 5. After 5 days, the cocultured group had more embryos in the blastocyst stage (69.8%) when compared with the control group (30%) (p < 0.001). It was also found that nearly 57% of blastocysts in the cocultured group reached the hatching stage, while only 13% achieved this stage in the control group (p < 0.001). Analyses of cultured mbMSCs and growth media, in the presence or absence of an embryo, were also performed. Immunofluorescence detected similar levels of collagen I and III and fibronectin in both mbMSCs and cocultured mbMSCs, and similar amounts of growth factors, VEGF, PDGF-AA, and PDGF-BB, were also observed in the conditioned medium, regardless of embryo presence. The present study describes, for the first time, an easy, noninvasive, and autologous method that could potentially increase blastocyst growth rates during assisted reproductive procedures (i.e., in vitro fertilization). It is proposed that this mbMSC coculture strategy enriches the embryonic microenvironment and promotes embryo development. This technique may complement or replace existing assisted reproduction methods and is directly relevant to the field of personalized medicine. Impact statement The study demonstrates a novel and potentially personalized assisted reproduction approach. The search for alternative and autologous methods provides assisted reproduction patients with a better chance of a successful pregnancy. In this study, mesenchymal cells derived from menstrual blood resembled the outside uterine surface and could potentially be employed for improving embryo outgrowth. Our protocol enriches the embryonic microenvironment and facilitates high-quality single-embryo transfer.

A Novel Human Placental Barrier Model Based on Trophoblast Stem Cells Derived from Human Induced Pluripotent Stem Cells

The placenta acts as an interface between the fetus and the expecting mother. Various drugs and environmental pollutants can pass through the human placental barrier and may harm the developing fetus. Currently available in vitro placental barrier models are often inadequate, because they are lacking the functional trophoblast cells. Therefore, we developed and characterized a new human placental model using trophoblast stem cells (TSCs) derived from human induced pluripotent stem cells. Umbilical vein endothelial cells, fibroblast, and TSCs were cocultured using micromesh cell culture technique. These cells formed a tight three-layered structure. This coculture model induced progressive fusion of TSCs and formed a syncytialized epithelium that resembles the in vivo syncytiotrophoblast. Our model allowed the cultured trophoblasts to form microvilli and to reconstitute expression and physiological localization of membrane transport proteins, such as transporter for ATP-binding cassette subfamily B member 1, ATP-binding cassette subfamily C member 3, and glucose transporter-1. Drug permeability assays were performed using five compounds. The results from the permeability assays were comparable to the ones obtained with ex vivo placental models. In conclusion, we developed a novel coculture model mimicking human placenta that provides a useful tool for the studies on transfer of substances between the mother and fetus. Impact statement Compared with the currently available in vitro placental barrier models, a novel three-dimensional coculture placental barrier model presented in this study morphologically and functionally modeled the true placental barrier. The use of human trophoblast stem cells from human induced pluripotent stem cells substantially improved the current model. The use of micromesh sheet as a bioscaffold facilitated the formation of a good multilayer structure, which is closer to the physical appearance of the placenta observed in human.

Renal tubular Bim mediates the tubule-podocyte crosstalk via NFAT2 to induce podocyte cytoskeletal dysfunction

Diabetic nephropathy (DN) is mainly regarded as diabetic glomerulopathy, and its progression is tightly correlated with tubular epithelial lesions. However, the underlying molecular mechanisms linking tubular damage and glomerulopathy are poorly understood.

Methods: We previously reported that the upregulation of Bim mediated proximal tubular epithelial cell (PTEC) apoptosis and was crucial in the early stages of DN. Herein we modulated Bim expression in PTECs and subsequently determined podocyte (PC) cytoskeletal arrangement by building a Transwell co-culture system in high glucose (HG).

Results: Compared to normal glucose, exposure to 40 mM of HG for 48 h induced significant expression of Bim in PTECs and disorganization in the PC cytoskeleton. When cocultured with PTECs in HG, exacerbated filamentous actin (F-actin) rearrangement and reduced synaptopodin levels were detected in PCs. In contrast, gene knockdown of Bim in PTECs was correlated with the absence of PC cytoskeletal disorganization. NFAT2 level and its nuclear translocation in PTECs were decreased by suppressing Bim expression. Upregulating NFAT2 disrupted the beneficial effects on F-actin organization in PCs obtained by inhibiting Bim. LncRNA microarray analysis identified NONHSAT179542.1, which was implicated in Bim-mediated PC cytoskeletal disorder.

Conclusion: Our study clarified the functional role of Bim, a pro-apoptotic factor, which is involved in the crosstalk between PTECs and PCs. Bim promotes NFAT2 activation in PTECs, inducing the downregulation of lncRNA NONHSAT179542.1 in PCs, contributing to the cytoskeletal damage. Identification of the role of the Bim/NFAT2 pathway may represent a promising research direction for a better understanding of DN development.

Human In Vitro Model Mimicking Material-Driven Vascular Regeneration Reveals How Cyclic Stretch and Shear Stress Differentially Modulate Inflammation and Matrix Deposition

Resorbable synthetic scaffolds designed to regenerate living tissues and organs inside the body have emerged as a clinically attractive technology to replace diseased blood vessels. However, mismatches between scaffold design and in vivo hemodynamic loading (i.e., cyclic stretch and shear stress) can result in aberrant inflammation and adverse tissue remodeling, leading to premature graft failure. Yet, the underlying mechanisms remain elusive. Here, a human in vitro model is presented that mimics the transient local inflammatory and biomechanical environments that drive scaffold-guided tissue regeneration. The model is based on the coculture of human (myo)fibroblasts and macrophages in a bioreactor platform that decouples cyclic stretch and shear stress. Using a resorbable supramolecular elastomer as the scaffold material, it is revealed that cyclic stretch initially reduces proinflammatory cytokine secretion and, especially when combined with shear stress, stimulates IL-10 secretion. Moreover, cyclic stretch stimulates downstream (myo)fibroblast proliferation and matrix deposition. In turn, shear stress attenuates cyclic-stretch-induced matrix growth by enhancing MMP-1/TIMP-1-mediated collagen remodeling, and synergistically alters (myo)fibroblast phenotype when combined with cyclic stretch. The findings suggest that shear stress acts as a stabilizing factor in cyclic stretch-induced tissue formation and highlight the distinct roles of hemodynamic loads in the design of resorbable vascular grafts.

PCL-Blended Chitosan Substrates for Patterning the Heterotypic Cell Distribution in an Epithelial and Mesenchymal Coculture System

Cell-cell and cell-substrate interactions in coculture systems are very important to the context of biomaterial scaffolds for tissue engineering applications. Understanding the cellular interactions and distribution of epithelial-mesenchymal microtissues on the controllable biomaterial surfaces is useful to study the organoid applications. The aim of the present study is to investigate the effects of chitosan/poly(ε-caprolactone) (PCL)-blended biomaterials on the distribution and spheroid formation of HaCaT and Hs68 cells in a coculture system. In this study, we demonstrated that the cocultured cells gradually changed their pattern from core/shell spheroid to monolayered morphology as the PCL content increased in the blended substrates. This indicates that the chitosan/PCL-blended substrates are able to regulate cell-substrate and cell-cell interactions to modify the distribution of HaCaT and Hs68 cells similar to various mesenchymal-epithelial organizations in biological tissues. Moreover, we also developed a two-dimension lattice model to elaborate the dependence of cell spheroid development on complex cell-cell interactions. This information may be helpful to develop appropriate biomaterials with appropriate properties to the applications of engineered epithelial-mesenchymal organoids.

Wright A. Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells

Interactions between lymphoma cells and stromal cells play a key role in promoting tumor survival and development of drug resistance. We identified differences in key signaling pathways between the JeKo-1 and REC-1 mantle cell lymphoma (MCL) cell lines, displaying different patterns of stromal cell adhesion and chemotaxis towards stroma-conditioned medium. The identified adhesion-regulated genes reciprocated important aspects of microenvironment-mediated gene modulation in MCL patients. Five-hundred and ninety genes were differently regulated between the cell lines upon adhesion to stromal cells, while 32 genes were similarly regulated in both cell lines. Regulation of B-cell Receptor (BCR) signature genes in adherent cells was specific for JeKo-1. Inhibition of BCR using siRNA or clinically approved inhibitors, Ibrutinib and Acalabrutinib, decreased adhesion of JeKo-1, but not REC-1 cells. Cell surface levels of chemokine receptor CXCR4 were higher in JeKo-1, facilitating migration and adhesion of JeKo-1 but not REC-1 cells. Surface levels of ICAM1 adhesion protein differ for REC-1 and JeKo-1. While ICAM1 played a positive role in adherence of both cell lines to stromal cells, S1PR1 had an inhibitory effect. Our results provide a model framework for further investigation of mechanistic differences in patient-response to new pathway-specific drugs.

Differentiation of Murine C2C12 Myoblasts Strongly Reduces the Effects of Myostatin on Intracellular Signaling

Alongside in vivo models, a simpler and more mechanistic approach is required to study the effects of myostatin on skeletal muscle because myostatin is an important negative regulator of muscle size. In this study, myostatin was administered to murine (C2C12) and human (CHQ) myoblasts and myotubes. Canonical and noncanonical signaling downstream to myostatin, related ligands, and their receptor were analyzed. The effects of tumorkines were analyzed after coculture of C2C12 and colon cancer-C26 cells. The effects of myostatin on canonical and noncanonical signaling were strongly reduced in C2C12 cells after differentiation. This may be explained by increased follistatin, an endogenous blocker of myostatin and altered expression of activin receptor ligands. In contrast, CHQ cells were equally responsive to myostatin, and follistatin remained unaltered. Both myostatin administration and the coculture stimulated pathways associated with inflammation, especially in C2C12 cells. In conclusion, the effects of myostatin on intracellular signaling may be cell line- or organism-specific, and C2C12 myotubes seem to be a nonoptimal in vitro model for investigating the effects of myostatin on canonical and noncanonical signaling in skeletal muscle. This may be due to altered expression of activin receptor ligands and their regulators during muscle cell differentiation.

Cooperative Response of Pichia kudriavzevii and Saccharomyces cerevisiae to Lactic Acid Stress in Baijiu Fermentation

Lactic acid is a universal metabolite, as well as a growth inhibitor of ethanol producers in Baijiu fermentation. Revealing the mechanism of lactic acid tolerance is essential for the yield of fermented foods. Here, we employed reverse transcription-quantitative polymerase chain reaction to explore the degradation mechanism of lactic acid, based on the coculture of Pichia kudriavzevii and Saccharomyces cerevisiae. Under high lactic acid stress, P. kudriavzevii decreased lactic acid from 40.00 to 35.46 g L^-1 within 24 h. Then, S. cerevisiae restored its capacity to degrade lactic acid. Finally, lactic acid decreased to 26.29 g L^-1. Coculture significantly enhanced lactic acid consumption compared to the monoculture of P. kudriavzevii (90% higher) or S. cerevisiae (209% higher). We found that lactate catabolism, H⁺ extrusion, and glycerol transport were the lactic acid tolerance pathways in yeasts. This study reveals the novel acid tolerance mechanisms of microbiota and would provide new strategies for ethanol production under acid stress.

Sustainable production of FAEE biodiesel using the oleaginous yeast Yarrowia lipolytica

Fatty acid ethyl esters (FAEEs) are fatty acid‐derived molecules and serve as an important form of biodiesel. The oleaginous yeast Yarrowia lipolytica is considered an ideal host platform for the production of fatty acid‐derived products due to its excellent lipid accumulation capacity. In this proof‐of‐principle study, several metabolic engineering strategies were applied for the overproduction of FAEE biodiesel in Y. lipolytica. Here, chromosome‐based co‐overexpression of two heterologous genes, namely, PDC1 (encoding pyruvate decarboxylase) and ADH1 (encoding alcohol dehydrogenase) from Saccharomyces cerevisiae, and the endogenous GAPDH (encoding glyceraldehyde‐3‐phosphate dehydrogenase) gene of Y. lipolytica resulted in successful biosynthesis of ethanol at 70.8 mg/L in Y. lipolytica. The engineered Y. lipolytica strain expressing the ethanol synthetic pathway together with a heterologous wax ester synthase (MhWS) exhibited the highest FAEE titer of 360.8 mg/L, which is 3.8‐fold higher than that of the control strain when 2% exogenous ethanol was added to the culture medium of Y. lipolytica. Furthermore, a synthetic microbial consortium comprising an engineered Y. lipolytica strain that heterologously expressed MhWS and a S. cerevisiae strain that could provide ethanol as a substrate for the production of the final product in the final engineered Y. lipolytica strain was created in this study. Finally, this synthetic consortium produced FAEE biodiesel at a titer of 4.8 mg/L under the optimum coculture conditions.

Nascent Lung Organoids Reveal Epithelium- and Bone Morphogenetic Protein-mediated Suppression of Fibroblast Activation

Reciprocal epithelial-mesenchymal interactions are pivotal in lung development, homeostasis, injury, and repair. Organoids have been used to investigate such interactions, but with a major focus on epithelial responses to mesenchyme and less attention to epithelial effects on mesenchyme. In the present study, we used nascent organoids composed of human and mouse lung epithelial and mesenchymal cells to demonstrate that healthy lung epithelium dramatically represses transcriptional, contractile, and matrix synthetic functions of lung fibroblasts. Repression of fibroblast activation requires signaling via the bone morphogenetic protein (BMP) pathway. BMP signaling is diminished after epithelial injury in vitro and in vivo, and exogenous BMP4 restores fibroblast repression in injured organoids. In contrast, inhibition of BMP signaling in healthy organoids is sufficient to derepress fibroblast matrix synthetic function. Our results reveal potent repression of fibroblast activation by healthy lung epithelium and a novel mechanism by which epithelial loss or injury is intrinsically coupled to mesenchymal activation via loss of repressive BMP signaling.

High-Content Screening, a Reliable System for Coxiella burnetii Isolation from Clinical Samples

Q fever, caused by Coxiella burnetii, is a worldwide zoonotic disease that may cause severe forms in humans and requires a specific and prolonged antibiotic treatment. Although current serological and molecular detection tools allow a reliable diagnosis of the disease, culture of C. burnetii strains is mandatory to assess their susceptibility to antibiotics and sequence their genome in order to optimize patient management and epidemiological studies. However, cultivating this fastidious microorganism is difficult and restricted to reference centers, as it requires biosafety level 3 laboratories and relies on cell culture performed by experienced technicians. In addition, the culture yield is low, which results in a small number of isolates being available. In this work, we developed a novel high-content screening (HCS) isolation strategy based on optimized high-throughput cell culture and automated microscopic detection of infected cells with specifically designed algorithms targeting cytopathic effects. This method was more efficient than the shell vial assay, at the level of time dependency, when applied to both frozen specimens (7 isolates recovered by HCS only, sensitivity 91% versus 78% for shell vial) and fresh samples (1 additional isolate using HCS, sensitivity 7% versus 5% for shell vial), for which most strains were recovered more rapidly with the new technique. In addition, detecting positive cultures by an automated microscope reduced the need for expertise and saved 24% of technician working time. Application of HCS to antibiotic susceptibility testing of 12 strains demonstrated that it was as efficient as the standard procedure that combines shell vial culture and quantitative PCR.

A Factor Produced by Kaistia sp. 32K Accelerated the Motility of Methylobacterium sp. ME121

Motile Methylobacterium sp. ME121 and non-motile Kaistia sp. 32K were isolated from the same soil sample. Interestingly, ME121 was significantly more motile in the coculture of ME121 and 32K than in the monoculture of ME121. This advanced motility of ME121 was also observed in the 32K culture supernatant. A swimming acceleration factor, which we named the K factor, was identified in the 32K culture supernatant, purified, characterized as an extracellular polysaccharide (5–10 kDa), and precipitated with 70% ethanol. These results suggest the possibility that the K factor was directly or indirectly sensed by the flagellar stator, accelerating the flagellar rotation of ME121. To the best of our knowledge, no reports describing an acceleration in motility due to coculture with two or more types of bacteria have been published. We propose a mechanism by which the increase in rotational force of the ME121 flagellar motor is caused by the introduction of the additional stator into the motor by the K factor.

Nasal Chondrocyte-Derived Soluble Factors Affect Chondrogenesis of Cocultured Mesenchymal Stem Cells

To investigate the effect of soluble factors released from human nasal chondrocytes (NCs) on cocultured human bone marrow mesenchymal stem cells (MSCs) and NC tissue-engineered constructs. Cartilage engineered from pure NCs on a three-dimensional (3D) porous collagen scaffold was cultured indirectly in a Transwell system with cartilage engineered from a direct coculture of human bone marrow-derived MSCs and NCs on a 3D porous collagen scaffold. The soluble factors were measured in the conditioned media from the different chambers of the Transwell system. Engineered cartilage from cocultures exposed to the pure NC construct exhibited reduced chondrogenic potential relative to control constructs, shown by reduced extracellular matrix deposition and increased expression of hypertrophic markers. Analysis of the soluble factors within the conditioned media showed an increase in inflammatory cytokines in the coculture chamber exposed to the pure NC construct. Principal component analysis revealed that the majority of the data variance could be explained by proinflammatory factors and hypertrophic chondrogenesis. In conclusion, our data suggest that inflammatory cytokines derived from NCs reduce the chondrogenic potential of coculture engineered cartilage through the induction of hypertrophic chondrogenesis. Impact statement The use of engineered cartilage from cocultured nasal chondrocytes (NCs) and mesenchymal stem cells for nasal cartilage reconstruction may be problematic. Our data suggest that the soluble factors from surrounding native NCs in the cartilage to be fixed can compromise the quality of the engineered cartilage if used in reconstructive surgery.

Coculture at the crossroads of the new microbiology techniques for the isolation of strict intracellular bacteria

Coculture played a major role in clinical microbiology by elucidating strict intracellular bacteria era. Since some of these bacteria are human pathogens, in-depth studies at the strain level are necessary to better understand their pathologies and treatment. Over the last decades, culture-independent tools have taken over the diagnostic procedure at the expense of coculture. These tools, although proven to be rapid and efficient, cannot overcome the need to culture the bacteria, as strain isolation remains a key factor to understanding its epidemiology, virulence and antibiotic susceptibility testing. Moreover, strain availability allows the development of molecular and serological tools, and remains crucial for taxonomy. This review revisits the current status of culture, its advantages, drawbacks and future needs.

Investigating E. coli Coculture for Resveratrol Production with 13C Metabolic Flux Analysis

Resveratrol, a phytoalexin produced by plants, has several beneficial effects in humans. It can be produced using Escherichia coli by introducing only three heterologous genes: TAL, 4CL, and STS. However, the resveratrol synthesis pathway requires two precursors, tyrosine and acetyl-CoA, which are produced by two branched central metabolic pathways. Therefore, overexpression of these genes in E. coli results in the production of only trace amounts of resveratrol. In this study, we attempted to produce resveratrol via coculture of two engineered strains in which the two metabolic pathways are activated. The first strain was engineered to produce p-coumaric acid using tyrosine as a precursor, which can be synthesized by the pentose phosphate pathway. The second strain produced resveratrol by combining p-coumaric acid from the first strain and malonyl-CoA synthesized from acetyl-CoA, which is produced by the glycolytic pathway. In total, 55.7 mg/L of resveratrol was produced from 20 g/L of glucose via coculture of these two strains in glucose minimal medium without any supplements. The metabolic fluxes in each of the strains producing resveratrol were successfully investigated by ¹³C metabolic flux analysis. The results showed that the balance between the citric acid cycle and the malonyl-CoA supply node was important for resveratrol production.

Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly

A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious levels. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1,590 isolates belonging to 102 species. This culture collection represents 34.57% of the taxonomic diversity and 70% functional capacity, as estimated by metagenomic sequencing of the fecal samples used for culture. Using whole-genome sequencing, we characterized species representatives from this collection and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profiles and short-chain fatty acid production. When screened with a coculture assay, 66 species in our culture collection inhibited Clostridioides difficile Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol, or succinate, correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile We tested 256 combinations and found that both species composition and blend size were important in inhibition. Our results show that the interaction of bacteria with one another in a mix and with other members of gut commensals must be investigated to design defined bacterial mixes for inhibiting C. difficile in vivo IMPORTANCE Antibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. The C. difficile-inhibiting species and bacterial combinations identified herein improve the understanding of the ecological interactions controlling colonization resistance against C. difficile and could aid in the design of defined bacteriotherapy as a nonantibiotic alternative against CDI.