Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx.

Strain ELA7T, a novel Gram-negative, non-motile bacterium with a white pigment and rod-shaped morphology, was isolated from the faeces of an eland at Seoul Grand Park, a zoo in the Republic of Korea. The novel bacterial strain grew optimally in R2A medium under the following conditions: 0 % (w/v) NaCl, pH 8.0, and 34 °C. Based on phylogenetic analyses using 16S rRNA gene sequencing, strain ELA7T was found to have the closest relatedness to Pedobacter ginsengisoli Gsoil 104T (97.8 %), P. frigoris RP-3-15T (97.2 %), P. humi THG S15-2T (97.0 %), P. seoulensis THG-G12T (97.0 %), and P. foliorum LMG 31463T (96.9 %). The genome size and genomic DNA G+C content of strain ELA7T were 3.63 Mbp and 46.5 %, respectively. A whole genome-level comparison of strain ELA7T with P. ginsengisoli Gsoil 104T, P. frigoris RP-3-15T, P. africanus DSM 12126T, and P. psychroterrae RP-1-14T revealed average nucleotide identity values of 72.0, 71.8, 71.9, and 71.6 %, respectively. The major fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and MK-7 was the predominant respiratory quinone. The major polar lipids of strain ELA7T were phosphatidylethanolamine, sphingolipid, unidentified aminolipid, unidentified phosphoglycolipid, unidentified glycolipid, and eight unidentified lipids. Considering our chemotaxonomic, genotypic, and phenotypic findings, strain ELA7T (=KACC 23137T=JCM 36003T) is identified as representing a novel species within the genus Pedobacter, for which the name Pedobacter faecalis sp. nov. is proposed.

Niabella defluvii sp. nov., isolated from influent water of a wastewater treatment plant.

Strain I65T (=KACC 22647T=JCM 35315T), a novel Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped, and orange-pigmented bacterium was isolated from influent water of a wastewater treatment system after treatment with several antibiotics, such as meropenem, gentamicin, and macrolide. The newly identified bacterial strain I65T exhibits significant multi-drug and heavy metal resistance characteristics. Strain I65T was grown in Reasoner's 2A medium [0 %-2 % (w/v) NaCl (optimum, 0 %), pH 5.0-10.0 (optimum, pH 7.0), and 20-45°C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain I65T was closely related to Niabella yanshanensis CCBAU 05354T (99.56 % sequence similarity), Niabella hibiscisoli THG-DN5.5T (97.51 %), and Niabella ginsengisoli GR10-1T (97.09 %). Further analysis of the whole-genome sequence confirmed that the digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain I65T and N. yanshanensis CCBAU 05354T were 23.4, 80.7, and 85.0 %, respectively, suggesting that strain I65T is distinct from N. yanshanensis. The genome size of strain I65T was 6.1 Mbp, as assessed using the Oxford Nanopore platform, and its genomic DNA G+C content was 43.0 mol%. The major fatty acids of strain I65T were iso-C15 : 0 and iso-C15 : 1 G, and the major respiratory quinone was MK-7. Moreover, the major polar lipid of strain I65T was phosphatidylethanolamine. Based on genotypic, chemotaxonomic, and phenotype data, strain I65T represents a novel species belonging to the genus Niabella, for which the name Niabella defluvii sp. nov. is proposed. The type strain is I65T (=KACC 22647T=JCM 35315T).

Kaistella rhinocerotis sp. nov., isolated from the faeces of rhinoceros and reclassification of Chryseobacterium faecale as Kaistella faecalis comb. nov.

Strain Ran72T, a novel Gram-stain-negative, obligately aerobic, non-motile, and rod-shaped bacterium, was isolated from the faeces of the rhinoceros species Ceratotherium simum. The novel bacterial strain grew optimally in Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5, and 30 °C. Based on phylogenetic analysis using 16S rRNA gene sequencing, strain Ran72T was found to be most closely related to Chryseobacterium faecale F4T (98.4 %), Kaistella soli DKR-2T (98.0 %), and Kaistella haifensis H38T (97.4 %). A comprehensive genome-level comparison between strain Ran72T with C. faecale F4T, K. soli DKR-2T, and K. haifensis H38T revealed average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values of ≤74.9, ≤19.3, and ≤78.7 %, respectively. The major fatty acids were anteiso-C15 : 0 (22.3 %), with MK-6 being the predominant respiratory quinone. The major polar lipids of strain Ran72T were phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. Based on our chemotaxonomic, genotypic, and phenotype characterizations, strain Ran72T was identified as representing a novel species in the genus Kaistella, for which the name Kaistella rhinocerotis sp. nov. is proposed, with the type strain Ran72T (=KACC 23136T=JCM 36038T). Based on the outcomes of our phylogenomic study, Chryseobacterium faecale should be reclassified under the genus Kaistella as Kaistella faecalis comb. nov.

Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress.

Both culture-independent and culture-dependent analyses using Nanopore-based 16S rRNA sequencing showed that short-term exposure of Antarctic soils to low temperature increased biomass with lower bacterial diversity and maintained high numbers of the phylum Proteobacteria, Firmicute, and Actinobacteria including Pseudarthrobacter species. The psychrophilic Pseudarthrobacter psychrotolerans YJ56 had superior growth at 13 °C, but could not grow at 30 °C, compared to other bacteria isolated from the same Antarctic soil. Unlike a single rod-shaped cell at 13 °C, strain YJ56 at 25 °C was morphologically shifted into a filamentous bacterium with several branches. Comparative genomics of strain YJ56 with other genera in the phylum Actinobacteria indicate remarkable copy numbers of rimJ genes that are possibly involved in dual functions, acetylation of ribosomal proteins, and stabilization of ribosomes by direct binding. Our proteomic data suggested that Actinobacteria cells experienced physiological stresses at 25 °C, showing the upregulation of chaperone proteins, GroEL and catalase, KatE. Level of proteins involved in the assembly of 50S ribosomal proteins and L29 in 50S ribosomal proteins increased at 13 °C, which suggested distinct roles of many ribosomal proteins under different conditions. Taken together, our data highlights the cellular filamentation and protein homeostasis of a psychrophilic YJ56 strain in coping with high-temperature stress.

Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria.

Animal fecal samples collected in the summer and winter from 11 herbivorous animals, including sable antelope (SA), long-tailed goral (LTG), and common eland (CE), at a public zoo were examined for the presence of antibiotic resistance genes (ARGs). Seven antibiotics, including meropenem and azithromycin, were used to isolate culturable multidrug-resistant (MDR) strains. The manures from three animals (SA, LTG, and CE) contained 104-fold higher culturable MDR bacteria, including Chryseobacterium, Sphingobacterium, and Stenotrophomonas species, while fewer MDR bacteria were isolated from manure from water buffalo, rhinoceros, and elephant against all tested antibiotics. Three MDR bacteria-rich samples along with composite samples were further analyzed using nanopore-based technology. ARGs including lnu(C), tet(Q), and mef(A) were common and often associated with transposons in all tested samples, suggesting that transposons carrying ARGs may play an important role for the dissemination of ARGs in our tested animals. Although several copies of ARGs such as aph(3')-IIc, blaL1, blaIND-3, and tet(42) were found in the sequenced genomes of the nine MDR bacteria, the numbers and types of ARGs appeared to be less than expected in zoo animal manure, suggesting that MDR bacteria in the gut of the tested animals had intrinsic resistant phenotypes in the absence of ARGs.

Transcriptomic Profiling Analysis of Castration-Resistant Prostate Cancer Cell Lines Treated with Chronic Intermittent Hypoxia.

Castration-resistant prostate cancer (CRPC) is still a major concern in men's health, with 375,000 cancer deaths annually. Hypoxia, which is a marked characteristic of advanced solid tumors, has been suggested to induce prostate cancer towards CRPC, metastasis and treatment resistance. To evaluate the effect of hypoxia on prostate cancer, two and five cycles of hypoxia and reoxygenation were administered using 22Rv1 cell lines and denominated as 22Rv1-CI and 22Rv1-PCI, respectively. Cancer cell migration was promoted in 22Rv1-CI compared to controls, and the expression of COL13A1 was significantly up-regulated in 22Rv1-CI according to differentially expressed gene analysis of RNA sequencing among groups. Cancer cell migration was impeded in a wound healing assay after transfecting si-COL13A1. Moreover, the expression of COL13A1 was also higher in the cell line originating from bone metastatic prostate cancer compared to other cell lines. Using the open database GEO, we also confirmed that the expression of COL13A1 was higher in bone metastatic prostate cancer tissue than in localized prostate cancer tissue in patients. Therefore, COL13A1 may be closely related to the bony metastasis of prostate cancer, and our findings may provide valuable information on the pathophysiology of the metastatic niche induced by hypoxia in patients with CRPC.

Chryseobacterium faecale sp. nov., isolated from camel feces.

Strain F4T (=KACC 22401T=JCM 34836T), a novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterium, was isolated from camel (Camelus bactrianus) faeces. The newly identified bacterial strain F4T was grown in Reasoner's 2A medium [0-2 % (w/v) NaCl (optimum, 0 %), pH 7.0-8.0 (optimum, pH 7.0), and 18-40 °C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain F4T belonged to the genus Chryseobacterium, with its closest neighbours being Chryseobacterium haifense DSM 19056T (98.0 %), Chryseobacterium anthropi CCUG 52764T (97.3 %), Chryseobacterium montana WG4T (95.7 %) and Chryseobacterium koreensis Chj70T (94.7 %). Complete genome sequence of strain F4T was obtained using a hybrid assembly pipeline integrating sequences obtained using both the Oxford Nanopore and Illumina platforms. Genomic comparisons of strain F4T with type species in the genus Chryseobacterium were conducted using digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity, resulting in values of ≤20.5, ≤77.9 and ≤80.8 %, respectively. The genomic DNA G+C content of type strain F4T was 39.7 mol%. The major fatty acids of the strain F4T were anteiso-C15 : 0 and iso-C18 : 3, and MK-6 was its major respiratory quinone. Moreover, the major polar lipid of strain F4T was phosphatidylethanolamine. The genome of strain F4T harbours only one antibiotic resistance gene (blaCME-1) encoding a ß-lactamase, which attributes ß-lactam antibiotic resistance. Based on the results of our chemotaxonomic, genotypic and phenotype analyses, strain F4T is identified as a novel species of the genus Chryseobacterium, for which the name Chryseobacterium faecale sp. nov. is proposed.

Use of Methylcellulose-Based Pellet to Enhance the Bacterial Self-Healing of Cement Composite.

In this study, a new type of bacterial carrier using methylcellulose was presented, and its applicability to self-healing concrete has been explored. Methylcellulose, the main component of a 2 mm pellet-shaped carrier, can remain stable in alkaline environments and expand in neutral or acidic environments. These properties allow bacteria to survive in the high-alkaline and high-pressure environments of early age concrete, and the number of bacteria increases rapidly in the event of cracks, accelerating crack closure. The results show that the survival rate of bacterial spores inside the mortar was increased, and the pellet provides an enhanced biological anchor suitable for bacterial activity, bacterial growth, and mineral precipitation. Further, the results indicate an improved self-healing efficiency compared with mixing bacteria directly into the cement composite.