Marnyiella aurantia, gen. nov., sp. nov., a novel bacterial species of the family Weeksellaceae that could produce flexirubin type pigments.

Two Gram-stain-negative, non-spore-forming, rod-shaped, and obligately aerobic bacteria, designated strains CX-624T and cx-311, were isolated from soil samples in Qinghai Province, China. The two strains grew best at 28 °C on the plate with Tryptone soya agar (TSA). Cells formed circular, convex, translucent, smooth, and orange colonies with approximately 1.0 mm diameter after 2 days of incubation on TSA at 28 °C. The strains were oxidase-negative and catalase-positive. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and major polar lipids included phosphatidylethanolamine, an unidentified aminophospholipid, four unidentified lipids and an aminolipid. MK-6 was the sole menaquinone in strain CX-624T. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed strains CX-624T and cx-311 were member of the family Weeksellaceae, with the highest similarity to Kaistella haifensis H38T (96.66 %), Epilithonimonas pallida DSM 18015T (96.59 %), and Chryseobacterium gambrini DSM 18014T (96.53 %). Both phylogenetic analysis of the 16S rRNA gene and 177 core genes revealed that strains CX-624T and cx-311 formed an independent clade. Average nucleotide identity values (< 72.64 %), average amino-acid identity values (<72.61 %) and digital DNA-DNA hybridization (< 21.10 %) indicated that the strains CX-624T and cx-311 should constitute a novel genus. The DNA G+C contents of strains CX-624T and cx-311 were 43.0 mol% and 42.7 mol%. According to the data obtained in this study, strain CX-624T represents a novel species belonging to a novel genus of the Weeksellaceae, for which the name Marnyiella aurantia gen. nov., sp. nov. is proposed. The type strain is CX-624T (=GDMCC 1.1714T = JCM 33925T).

Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov., isolated from bat faeces.

Four mesophilic actinobacteria (HY002T, HY442, HY366T and HY285) isolated from the faeces of bats collected in southern China were found to be strictly aerobic, non-motile, rod-shaped, oxidase-negative, Gram-stain-positive and catalase-positive. Strains HY002T and HY366T contained meso-diaminopimelic acid as the diagnostic diamino acid and MK-9(H2) the sole respiratory quinone. Arabinose, galactose and ribose were detected in the whole-cell hydrolysates of both type strains. The main cellular fatty acids (> 10.0%) of all strains were C16 : 0, C18 : 1 ω9c, 10-methyl-C18 : 0 and summed feature 3. Strains HY002T and HY366T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidyl inositol mannosides as the major polar lipids. The phylogenetic/phylogenomic analyses based on 16S rRNA gene and genomic sequence comparison revealed that the four strains belong to the genus Gordonia, most closely related to G. neofelifaecis NRRL B-59395T(98.2-98.3% sequence similarity) on the EzBioCloud database. The G+C contents of strains HY002T and HY366T based on genomic DNA were 66.5 and 66.9%, respectively. The DNA-DNA relatedness values between the two types strains and members of the genus Gordonia were far below 70 % (18.6-23.1 %). All genotypic and phenotypic data indicated that the four strains are representatives of two novel separate species, for which the names Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov. are proposed, with HY002T (=CGMCC 4 7757T=JCM 34 878T) and HY366T (=CGMCC 1 19146T=JCM 34 879T) as the respective type strains.

Genome characterization of Shewanella algae in Hainan Province, China.

Shewanella algae is an emerging marine zoonotic pathogen. In this study, we first reported the Shewanella algae infections in patients and animals in Hainan Province, China. Currently, there is still relatively little known about the whole-genome characteristics of Shewanella algae in most tropical regions, including in southern China. Here, we sequenced the 62 Shewanella algae strains isolated from Hainan Province and combined with the whole genomes sequences of 144 Shewanella algae genomes from public databases to analyze genomic features. Phylogenetic analysis revealed that Shewanella algae is widely distributed in the marine environments of both temperate and tropical countries, exhibiting close phylogenetic relationships with genomes isolated from patients, animals, and plants. Thereby confirming that exposure to marine environments is a risk factor for Shewanella algae infections. Average nucleotide identity analysis indicated that the clonally identical genomes could be isolated from patients with different sample types at different times. Pan-genome analysis identified a total of 21,909 genes, including 1,563 core genes, 8,292 strain-specific genes, and 12,054 accessory genes. Multiple putative virulence-associated genes were identified, encompassing 14 categories and 16 subcategories, with 171 distinct virulence factors. Three different plasmid replicon types were detected in 33 genomes. Eleven classes of antibiotic resistance genes and 352 integrons were identified. Antimicrobial susceptibility testing revealed a high resistance rate to imipenem and colistin among the strains studied, with 5 strains exhibiting multidrug resistance. However, they were all sensitive to amikacin, minocycline, and tigecycline. Our findings clarify the genomic characteristics and population structure of Shewanella algae in Hainan Province. The results offer insights into the genetic basis of pathogenicity in Shewanella algae and enhance our understanding of its global phylogeography.

Species-level microbiota of ticks and fleas from Marmota himalayana in the Qinghai-Tibet Plateau.

Introduction: Ticks and fleas, as blood-sucking arthropods, carry and transmit various zoonotic diseases. In the natural plague foci of China, monitoring of Yersinia pestis has been continuously conducted in Marmota himalayana and other host animals, whereas other pathogens carried by vectors are rarely concerned in the Qinghai-Tibet Plateau. Methods: In this study, we investigated the microbiota of ticks and fleas sampling from M. himalayana in the Qinghai-Tibet Plateau, China by metataxonomics combined with metagenomic methods. Results: By metataxonomic approach based on full-length 16S rDNA amplicon sequencing and operational phylogenetic unit (OPU) analyses, we described the microbiota community of ticks and fleas at the species level, annotated 1,250 OPUs in ticks, including 556 known species and 492 potentially new species, accounting for 48.50% and 41.71% of the total reads in ticks, respectively. A total of 689 OPUs were detected in fleas, consisting of 277 known species (40.62% of the total reads in fleas) and 294 potentially new species (56.88%). At the dominant species categories, we detected the Anaplasma phagocytophilum (OPU 421) and potentially pathogenic new species of Wolbachia, Ehrlichia, Rickettsia, and Bartonella. Using shotgun sequencing, we obtained 10 metagenomic assembled genomes (MAGs) from vector samples, including a known species (Providencia heimbachae DFT2), and six new species affliated to four known genera, i.e., Wolbachia, Mumia, Bartonella, and Anaplasma. By the phylogenetic analyses based on full-length 16S rRNA genes and core genes, we identified that ticks harbored pathogenic A. phagocytophilum. Moreover, these potentially pathogenic novel species were more closely related to Ehrlichia muris, Ehrlichia muris subsp. eauclairensis, Bartonella rochalimae, and Rickettsia limoniae, respectively. The OPU 422 Ehrlichia sp1 was most related to Ehrlichia muris and Ehrlichia muris subsp. eauclairensis. The OPU 230 Bartonella sp1 and Bartonella spp. (DTF8 and DTF9) was clustered with Bartonella rochalimae. The OPU 427 Rickettsia sp1 was clustered with Rickettsia limoniae. Discussion: The findings of the study have advanced our understanding of the potential pathogen groups of vectors in marmot (Marmota himalayana) in the Qinghai-Tibet Plateau.

A novel bat coronavirus with a polybasic furin-like cleavage site.

The current pandemic of COVID-19 caused by a novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), threatens human health around the world. Of particular concern is that bats are recognized as one of the most potential natural hosts of SARS-CoV-2; however, coronavirus ecology in bats is still nascent. Here, we performed a degenerate primer screening and next-generation sequencing analysis of 112 bats, collected from Hainan Province, China. Three coronaviruses, namely bat betacoronavirus (Bat CoV) CD35, Bat CoV CD36 and bat alphacoronavirus CD30 were identified. Bat CoV CD35 genome had 99.5% identity with Bat CoV CD36, both sharing the highest nucleotide identity with Bat Hp-betacoronavirus Zhejiang2013 (71.4%), followed by SARS-CoV-2 (54.0%). Phylogenetic analysis indicated that Bat CoV CD35 formed a distinct clade, and together with Bat Hp-betacoronavirus Zhejiang2013, was basal to the lineage of SARS-CoV-1 and SARS-CoV-2. Notably, Bat CoV CD35 harbored a canonical furin-like S1/S2 cleavage site that resembles the corresponding sites of SARS-CoV-2. The furin cleavage sites between CD35 and CD36 are identical. In addition, the receptor-binding domain of Bat CoV CD35 showed a highly similar structure to that of SARS-CoV-1 and SARS-CoV-2, especially in one binding loop. In conclusion, this study deepens our understanding of the diversity of coronaviruses and provides clues about the natural origin of the furin cleavage site of SARS-CoV-2.

Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces.

Two strictly aerobic, Gram-staining-positive, non-spore-forming, regular rod-shaped (approximately 0.7 × 1.9 mm) bacteria (HY170T and HY001) were isolated from bat feces collected from Chongzuo city, Guangxi province (22°20'54″N, 106°49'20″E, July 2011) and Chuxiong Yi Autonomous Prefecture, Yunnan province (25°09'10″N, 102°04'39″E, October 2013) of South China, respectively. Optimal growth is obtained at 25-28°C (range, 4-32°C) on BHI-5% sheep blood plate with pH 7.5 (range, 5.0-10.0) in the presence of 0.5-1.0% NaCl (w/v) (range, 0-15% NaCl [w/v]). The phylogenetic and phylogenomic trees based respectively on the 16S rRNA gene and 845 core gene sequences revealed that the two strains formed a distinct lineage within the genus Brevibacterium, most closely related to B. aurantiacum NCDO 739T (16S rRNA similarity, both 98.5%; dDDH, 46.7-46.8%; ANI, 91.9-92.1%). Strain HY170T contained MK-8(H2), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), galactose and ribose as the predominant menaquinone, major polar lipids, and main sugars in the cell wall teichoic acids, respectively. The meso-diaminopimelic acid (meso-DAP) was the diagnostic diamino acid of the peptidoglycan found in strain HY170T. Anteiso-C15:0 and anteiso-C17:0 were the major fatty acids (> 10%) of strains HY170T and HY001, with anteiso-C17:1A predominant in strain HY170T but absent in strain HY001. Mining the genomes revealed the presence of secondary metabolite biosynthesis gene clusters encoding for non-alpha poly-amino acids (NAPAA), ectoine, siderophore, and terpene. Based on results from the phylogenetic, chemotaxonomic and phenotypic analyses, the two strains could be classified as a novel species of the genus Brevibacterium, for which the name Brevibacterium zhoupengii sp. nov. is proposed (type strain HY170T = CGMCC 1.18600T = JCM 34230T).

Creation of engineered cardiac tissue in vitro from mouse embryonic stem cells.

BACKGROUND: Embryonic stem (ES) cells can terminally differentiate into all types of somatic cells and are considered a promising source of seed cells for tissue engineering. However, despite recent progress in in vitro differentiation and in vivo transplantation methodologies of ES cells, to date, no one has succeeded in using ES cells in tissue engineering for generation of somatic tissues in vitro for potential transplantation therapy. METHODS AND RESULTS: ES-D3 cells were cultured in a slow-turning lateral vessel for mass production of embryoid bodies. The embryoid bodies were then induced to differentiate into cardiomyocytes in a medium supplemented with 1% ascorbic acid. The ES cell-derived cardiomyocytes were then enriched by Percoll gradient centrifugation. The enriched cardiomyocytes were mixed with liquid type I collagen supplemented with Matrigel to construct engineered cardiac tissue (ECT). After in vitro stretching for 7 days, the ECT can beat synchronously and respond to physical and pharmaceutical stimulation. Histological, immunohistochemical, and transmission electron microscopic studies further indicate that the ECTs both structurally and functionally resemble neonatal native cardiac muscle. Markers related to undifferentiated ES cell contamination were not found in reverse transcriptase-polymerase chain reaction analysis of the Percoll-enriched cardiomyocytes. No teratoma formation was observed in the ECTs implanted subcutaneously in nude mice for 4 weeks. CONCLUSIONS: ES cells can be used as a source of seed cells for cardiac tissue engineering. Additional work remains to demonstrate engraftment of the engineered heart tissue in the case of cardiac defects and its functional integrity within the host's remaining healthy cardiac tissue.

Construction of a unidirectionally beating 3-dimensional cardiac muscle construct.

BACKGROUND: Cardiac tissue engineering aims to construct cardiac tissue with characteristics similar to those of the native tissue. Engineered cardiac tissues (ECTs) can be constructed using synthetic scaffold or liquid collagen. We report an initial study using our own newly designed cardiac muscle device to construct heart tissue. We investigated the effects of cell seeding density and collagen quantity on the formation of liquid collagen-based cardiac muscle. METHODS: We obtained cardiac myocytes from neonatal rats mixed with collagen type I and matrix factors cast in circular molds to form circular strands. Cell densities (0.1 x 10(7) to 6 x 10(7)) and collagen quantity (0.3 to 1.0 ml/ECT) were tested. Cell gross morphology, cell orientation, spatial distribution and ultrastructure were evaluated using histologic analyses, confocal laser scanning microscopy and transmission electron microscopy. RESULTS: Histologic analyses of ECTs revealed that cardiac cells reconstituted longitudinally oriented, cardiac bundles with morphologic features characteristic of the native tissue. Confocal and electron microscopy demonstrated that, using optimized cell density and collagen quantity, we made ECTs with characteristic features similar to those of native differentiated myocardium. CONCLUSIONS: ECTs comparable to native cardiac tissue can be engineered under optimized conditions. This construct is a first step in the development of cardiac tissue engineered in vitro, and may be used as a basis for studies of cardiac development, drug testing and tissue replacement therapy.

Repair of large articular cartilage defects with implants of autologous mesenchymal stem cells seeded into beta-tricalcium phosphate in a sheep model.

Tissue engineering has long been investigated to repair articular cartilage defects. Successful reports have usually involved the seeding of autologous chondrocytes into polymers. Problems arise because of the scarcity of cartilage tissue biopsy material, and because the in vitro expansion of chondrocytes is difficult; to some extent, these problems limit the clinical application of this promising method. Bone marrow-derived mesenchymal stem cells (MSCs) have been proved a potential cell source because of their in vitro proliferation ability and multilineage differentiation capacity. However, in vitro differentiation will lead to high cost and always results in decreased cell viability. In this study we seeded culture-expanded autologous MSCs into bioceramic scaffold-beta-tricalcium phosphate (beta-TCP) in an attempt to repair articular cartilage defects (8 mm in diameter and 4 mm in depth) in a sheep model. Twenty-four weeks later, the defects were resurfaced with hyaline-like tissue and an ideal interface between the engineered cartilage, the adjacent normal cartilage, and the underlying bone was observed. From 12 to 24 weeks postimplantation, modification of neocartilage was obvious in the rearrangement of surface cartilage and the increase in glycosaminoglycan level. These findings suggest that it is feasible to repair articular cartilage defects with implants generated by seeding autologous MSCs, without in vitro differentiation, into beta-TCP. This approach provides great potential for clinical applications.

Repair of osteochondral defects with autologous chondrocytes seeded onto bioceramic scaffold in sheep.

At present, the most popular biomaterials used in cartilage tissue engineering are synthetic polymers. However, problems-such as acidic by-product accumulation and side effects in local or systemic inflammatory reactions during in vivo degradation-are drawing much attention. The polymers are also highly hydrophobic and degrade within 4 weeks, allowing insufficient time to support neocartilage formation. All these have made polymers less promising in clinical application. In this study, we tested a new bioceramic scaffold made of artificial synthesized powder of beta-tricalcium phosphate (beta-TCP) in a sheep model. Osteochondral defects were filled with a bioceramic-chondrocyte construct and neocartilage tissue completely resurfaced the cartilage defects after 24 weeks. Typical hyaline cartilage structure was generated in the engineered cartilage. Biodegradation of bioceramic was notable, leading to bioceramic fragmentation and particle formation. Numerous ceramic particles (size, 0.5-1.9 microm) and numerous macrophages were observed at the ceramic-tissue interface as well as in the marrow tissue. No macrophages were visible in the neocartilage tissue. Although long-term in vivo study is needed to further determine the pathological sequences of the beta-TCP-based cartilage construct, this study suggests that this bioceramic might be used to repair chondral or osteochondral defects and could be used as a scaffold for cartilage tissue engineering.

[Experimental study of tissue-engineered heart tissue using type I collagen as scaffold].

OBJECTIVE: To construct tissue-engineered heart tissue (EHT) using liquid collagen as scaffold. METHODS: Neonatal rat cardiac myocytes were isolated, cultured, and mixed with liquid collagen type I and matrix factors and then cast in circular molds to construct circular cardiac myocytes/collagen strand. After a 7-day culture in circular molds, the strands were removed, and subjected to 10% static stretch for another 7 days. Microscopy and transmission electron microscopy, routine HE staining and immunohistochemical staining were used to analyze the engineered heart tissue. RESULTS: Beating areas could be seen on the surface of the EHTs at the second day after stretching; more beating areas could be seen thereafter. These areas beat stronger and stronger, and finally came to synchronzation. Histological and immunohistochemical analyses showed that the cardiac myocytes in the EHTs distributed evenly in the whole strand and the majority of the cells, with elongated nuclei, stretched along the stretching direction. The morphology of EHTs resembled that of the native adult cardiac tissue. Transmission electron microscopy revealed that the cardiac myocytes in EHTs contained arranged myofibrils oriented parallel to the longitudinal cell axis. Clearly defined sarcomeres and Z lines were observed. CONCLUSION: Liquid type I collagen is a good scaffold for generation of EHTs similar to the native heart tissue.

In vivo chondrogenesis of adult bone-marrow-derived autologous mesenchymal stem cells.

The purpose of this study has been to investigate the possible effects of the normal joint cavity environment on chondrocytic differentiation of bone-marrow-derived mesenchymal stem cells (MSCs). Autologous bone marrow was aspirated from the iliac crest of male sheep. MSCs were purified, expanded, and labeled with the fluorescent dye PKH26. Labeled MSCs were then grown on a three-dimensional porous scaffold of poly (L-lactic-co-glycolic acid) in vitro and implanted into the joint cavity by a surgical procedure. At 4 or 8 weeks after implantation, the implants were removed for histochemical and immunohistochemical analysis. The cells labeled with red fluorescent PKH26 in the implants expressed type II collagen and synthesized sulfated proteoglycans. However, the osteoblast-specific marker, osteocalcin, was not detected by immunohistochemistry indicating that the implanted MSCs had not differentiated into osteoblasts by being directly exposed to the normal joint cavity. To investigate the possible factors involved in chondrocytic differentiation of MSCs further, we co-cultured sheep MSCs with the main components of the normal joint cavity, viz., synovial fluid or synovial cells, in vitro. After 1 or 2 weeks of co-culture, the MSCs in both co-culture systems expressed markers of chondrogenesis. These results suggest that synovial fluid and synovium from normal joint cavity are important for the chondrocytic differentiation of adult bone-marrow-derived MSCs.