Polycladomyces zharkentensis sp. nov., a novel thermophilic cellulose- and starch-degrading member of the Bacillota from a geothermal aquifer in Kazakhstan.

A thermophilic, aerobic and heterotrophic filamentous bacterium, designated strain ZKZ2T, was isolated from a pipeline producing hydrothermal water originating from a >2.3 km deep subsurface geothermal source in Zharkent, Almaty region, Kazakhstan. The isolate was Gram-stain-positive, non-motile, heat-resistant and capable of producing a variety of extracellular hydrolases. Growth occurred at temperatures between 55 and 75 °C, with an optimum around 70 °C, and at pH values between 5.5 and 9.0, with an optimum at pH 7.0-7.5 with the formation of aerial mycelia; endospores were produced along the aerial mycelium. The isolate was able to utilize the following substrates for growth: glycerol, l-arabinose, ribose, d-xylose, d-glucose, d-fructose, d-mannose, rhamnose, d-mannitol, methyl-d-glucopyranoside, aesculin, salicin, cellobiose, maltose, melibiose, sucrose, trehalose, melezitose, raffinose, starch, turanose and 5-keto-gluconate. Furthermore, it was able to hydrolyse carboxymethylcellulose, starch, skimmed milk, Tween 60 and Tween 80. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. Our 16S rRNA gene sequence analysis placed ZKZ2T within the genus Polycladomyces, family Thermoactinomycetaceae, with the highest similarity to the type species Polycladomyces abyssicola JIR-001T (99.18 % sequence identity). Our draft genome sequence analysis revealed a genome size of 3.3 Mbp with a G+C value of 52.5 mol%. The orthologous average nucleotide identity value as compared to that of its closest relative, P. abyssicola JIR-001T, was 90.23 %, with an in silico DNA-DNA hybridization value of 40.7 %, indicating that ZKZ2T represents a separate genome species. Based on the phenotypic and genome sequence differences from the other two Polycladomyces species, we propose that strain ZKZ2T represents a novel species, for which we propose the name Polycladomyces zharkentensis sp. nov. The type strain is ZKZ2T (=CECT 30708T=KCTC 43421T).

Draft Genome Sequence of Agrobacterium radiobacter Strain MD22b, Isolated from a Grape Plant in Tajikistan.

Agrobacterium radiobacter strain MD22b was isolated from infected fruit from Vatan Farm, a dekhkan farm in Yangibog (Tursunzade, Tajikistan). The 5.7-Mbp draft genome sequence presented here shares homology with chromosomes 1 and 2, as well as with the Ti plasmid from agrobacteria.

Fervidobacterium pennivorans subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile.

Fervidobacterium pennivorans subsp. keratinolyticus subsp. nov. strain T was isolated from a terrestrial, high-altitude hot spring in Tajikistan. This strain is an obligate anaerobic rod and their cells occur singly, in pairs, or as short chains under the optimal growth conditions of a temperature of 65 °C and pH 6.5, with peptone, glucose, and galactose as the preferred substrates. The minimum generation time of this strain is 150 min. Strain T can efficiently degrade feather keratin at 65-75 °C; this unusual feature is also exhibited by a few other members of the Fervidobacterium genus. The total genome size of this bacterial strain is 2,002,515 base pairs, with a C + G content of 39.0%. The maximum digital DNA-DNA hybridization (dDDH) value of 76.9% was observed on comparing the genome of this strain with that of Fervidobacterium pennivorans type strain DSM9078. This study describes the physiological and genomic properties of strain T, with an emphasis on its keratinolytic power and differences from other members of the genus Fervidobacterium.

Analysis of Salivary Mycobiome in a Cohort of Oral Squamous Cell Carcinoma Patients From Sudan Identifies Higher Salivary Carriage of Malassezia as an Independent and Favorable Predictor of Overall Survival.

Background: Microbial dysbiosis and microbiome-induced inflammation have emerged as important factors in oral squamous cell carcinoma (OSCC) tumorigenesis during the last two decades. However, the "rare biosphere" of the oral microbiome, including fungi, has been sparsely investigated. This study aimed to characterize the salivary mycobiome in a prospective Sudanese cohort of OSCC patients and to explore patterns of diversities associated with overall survival (OS). Materials and Methods: Unstimulated saliva samples (n = 72) were collected from patients diagnosed with OSCC (n = 59) and from non-OSCC control volunteers (n = 13). DNA was extracted using a combined enzymatic-mechanical extraction protocol. The salivary mycobiome was assessed using a next-generation sequencing (NGS)-based methodology by amplifying the ITS2 region. The impact of the abundance of different fungal genera on the survival of OSCC patients was analyzed using Kaplan-Meier and Cox regression survival analyses (SPPS). Results: Sixteen genera were identified exclusively in the saliva of OSCC patients. Candida, Malassezia, Saccharomyces, Aspergillus, and Cyberlindnera were the most relatively abundant fungal genera in both groups and showed higher abundance in OSCC patients. Kaplan-Meier survival analysis showed higher salivary carriage of the Candida genus significantly associated with poor OS of OSCC patients (Breslow test: p = 0.043). In contrast, the higher salivary carriage of Malassezia showed a significant association with favorable OS in OSCC patients (Breslow test: p = 0.039). The Cox proportional hazards multiple regression model was applied to adjust the salivary carriage of both Candida and Malassezia according to age (p = 0.029) and identified the genus Malassezia as an independent predictor of OS (hazard ratio = 0.383, 95% CI = 0.16-0.93, p = 0.03). Conclusion: The fungal compositional patterns in saliva from OSCC patients were different from those of individuals without OSCC. The fungal genus Malassezia was identified as a putative prognostic biomarker and therapeutic target for OSCC.

Metagenomics and Culture-Based Diversity Analysis of the Bacterial Community in the Zharkent Geothermal Spring in Kazakhstan.

Diversity of the microbial community in the Zharkent geothermal hot spring, located in the southeastern region of Kazakhstan, was assessed using both culture-dependent and -independent approaches. Shotgun metagenomic sequencing of DNA extracted from the spring water yielded 11,061,725 high-quality sequence reads, totaling >1,67 Gb of nucleotide sequences. Furthermore, water samples were enriched in nutrient broth at varying high temperatures, and colonies isolated by being streaked onto nutrient agar. Finally, DNA extraction and amplification, as well as sequencing and phylogenetic analysis, were conducted. Bacteria constituted more than 99.97% of the total prokaryotic abundance, with Archaea contributing only an extremely small component; Firmicutes, Proteobacteria, and Actinobacteria dominated the community. At genus level, Firmicutes reads affiliated with Desmospora, Parageobacillus, Paenibacillus, and Brevibacillus, accounting for more than 60% of total prokaryotic abundance. Eight morphologically distinct, aerobic, endospore-forming thermophilic bacteria were recovered; isolates differed significantly in substrate utilization patterns, as well as their production of thermophilic, extracellular, hydrolytic enzymes for degradation of starch, lipids, cellulose, and protein. Five strains could degrade all four macromolecular types at temperatures ranging from 55 to 75 °C. Phylogenetic analyses based on 16S rRNA gene sequences placed all isolates into the genus Geobacillus with some of them possibly representing novel species. The results indicate that this hot spring represents a rich source of novel thermophilic bacteria and potentially useful thermostable enzymes.