Cellulomonas shaoxiangyii sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Cellulomonas dongxiuzhuiae sp. nov., Cellulomonas wangleii sp. nov. and Cellulomonas fengjieae sp. nov., isolated from the intestinal contents of Marmota himalayana

Six Gram-stain-positive, aerobic or facultative anaerobic, catalase-positive, urease- and oxidase-negative, rod-shaped bacteria (zg-ZUI157T/zg-ZUI40, zg-ZUI222T/zg-ZUI199 and zg-ZUI188T/ zg-ZUI168) were characterized by a polyphasic approach. Optimal growth of the six strains was observed at pH 7.0 and 28 °C. Phylogenetic analyses based on the 16S rRNA gene and 247 core genes revealed that they belong to genus Cellulomonas . The three type strains have low digital DNA-DNA hybridization (19.3–30.1%) and average nucleotide identity values (78.0-85.5%) with all available genomes in the genus Cellulomonas , and a DNA G+C content range of 73.0-74.6 mol%. The major fatty acids detected in strain pairs zg-ZUI157T/zg-ZUI40 and zg-ZUI 222T/zg-ZUI199 were C16:0, anteiso-C15:0 and anteiso A-C15:1, and C16:0, anteiso-C15:0, anteiso A-C15:1 and anteiso-C17:0 in strain pair zg-ZUI188T/zg-ZUI168. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides were the major polar lipids detected in the three novel species. MK-9(H4) was the predominant quinone detected in strains zg-ZUI222T (87.4 %) and zg-ZUI188T (91.4 %), and MK-9(H4) (49.1 %) and MK-8 (43.4 %) in strain zg-ZUI157T. The cell-wall sugars detected in the three novel species mainly contained rhamnose. The cell-wall peptidoglycan type of the three novel species was A4β, with an inferred l-Orn–d-Asp interpeptide bridge for strains zg-ZUI157T and zg-ZUI222T, and l-Orn–d-Glu for strain zg-ZUI188T. Based on the results of the phenotypic, phylogenetic, genomic hybridization, average nucleotide identity and chemotaxonomic analyses, the six strains should be classified as belonging to three novel Cellulomonas species, for which the names Cellulomonas dongxiuzhuiae sp. nov. (zg-ZUI157T=GDMCC 1.2559T=KCTC 49678T), Cellulomonas wangleii sp. nov. (zg-ZUI222T=GDMCC 1.2501T=KCTC 49675T) and Cellulomonas fengjieae sp. nov. (zg-ZUI188T=GDMCC 1.2563T=KCTC 49674T) are proposed.

Chitin-Active Lytic Polysaccharide Monooxygenases Are Rare in Cellulomonas Species

Cellulomonas flavigena is a saprotrophic bacterium that encodes, within its genome, four predicted lytic polysaccharide monooxygenases (LPMOs) from Auxiliary Activity family 10 (AA10). We showed previously that three of these cleave the plant polysaccharide cellulose by oxidation at carbon-1 (J. Li, L. Solhi, E.D. Goddard-Borger, Y. Mattieu et al., Biotechnol Biofuels 14:29, 2021, https://doi.org/10.1186/s13068-020-01860-3). Here, we present the biochemical characterization of the fourth C. flavigena AA10 member (CflaLPMO10D) as a chitin-active LPMO. Both the full-length CflaLPMO10D-Carbohydrate-Binding Module family 2 (CBM2) and catalytic module-only proteins were produced in Escherichia coli using the native general secretory (Sec) signal peptide. To quantify chitinolytic activity, we developed a high-performance anion-exchange chromatography-pulsed amperometric detection (HPAEC-PAD) method as an alternative to the established hydrophilic interaction liquid ion chromatography coupled with UV detection (HILIC-UV) method for separation and detection of released oxidized chito-oligosaccharides. Using this method, we demonstrated that CflaLPMO10D is strictly active on the β-allomorph of chitin, with optimal activity at pH 5 to 6 and a preference for ascorbic acid as the reducing agent. We also demonstrated the importance of the CBM2 member for both mediating enzyme localization to substrates and prolonging LPMO activity. Together with previous work, the present study defines the distinct substrate specificities of the suite of C. flavigena AA10 members. Notably, a cross-genome survey of AA10 members indicated that chitinolytic LPMOs are, in fact, rare among Cellulomonas bacteria. IMPORTANCE Species from the genus Cellulomonas have a long history of study due to their roles in biomass recycling in nature and corresponding potential as sources of enzymes for biotechnological applications. Although Cellulomonas species are more commonly associated with the cleavage and utilization of plant cell wall polysaccharides, here, we show that C. flavigena produces a unique lytic polysaccharide monooxygenase with activity on β-chitin, which is found, for example, in arthropods. The limited distribution of orthologous chitinolytic LPMOs suggests adaptation of individual cellulomonads to specific nutrient niches present in soil ecosystems. This research provides new insight into the biochemical specificity of LPMOs in Cellulomonas species and related bacteria, and it raises new questions about the physiological function of these enzymes.

Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species

Four bacterial strains (LJ126^T/S18 and Z-34^T/S20) recovered from faecal samples of Tibetan antelopes on the Qinghai-Tibet Plateau of China were analysed using a polyphasic approach. All four isolates were aerobic, short rod-shaped, non-motile, Gram-stain-positive, acid-fast and fast-growing. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the two pair of strains formed two distinct branches within the evolutionary radiation of the genus Mycolicibacterium. Strains LJ126^T/S18 and Z-34^T/S20 were most closely related to Mycolicibacterium austroafricanum CCUG 37667^T, Mycobacterium aurum NCTC 10437^T, Mycobacterium pyrenivorans DSM 44605^T, Mycobacterium monacense JCM 15658^T, Mycolicibacterium sarraceniae JCM 30395^T, Mycolicibacterium tokaiense JCM 6373^T and Mycobacterium murale JCM 13392^T, but readily distinguished from the known species by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity values (74.4-84.9 %). Consequently, the two strain pairs are considered to represent different novel species of Mycolicibacterium for which the names Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov. are proposed, with LJ126^T (=CGMCC 1.1992^T=KCTC 49535^T) and Z-34^T (=CGMCC 1.1993^T=DSM 106172^T) as the respective type strains.

Cellulomonas taurus sp. nov., a novel bacteria with multiple hydrolase activity isolated from livestock, and potential application in wastewater treatment

A Gram-positive, smooth, sub-transparent, faint yellow,0.5-0.7 µm diameter, rod shaped aerobic or facultative aerobic strain P40-2^Twas isolated from livestock farms in Northeast China. Strain P40-2^T grew at 25-40 °C (optimum 30-38 °C), and in 0-4% (w/v) NaCl (optimum 0%) in LB medium. Based on 16S rRNA gene sequence analysis, strain P40-2^T belongs to the class Cellulomonas and is most closely related to C. denverensis strain W6929, C. pakistanensis strain NCCP-11and C. hominis strain CE40.DNA-DNA hybridization rate of strain P40-2^T was 29%, and the ANI with C.denverensisstrainW6929 was 85.33%. The genome is 3437431 bp long with a G + C content of 71.99%. Of the 3177 predicted genes, 3119 were protein-coding genes and 58 were RNA encoding genes. The chemotaxonomic data: menaquinone was MK-9(H₄), anteiso-C_15: 0, C_16:0 and anteiso-C_17: 0 were the major cellular fatty acids, and the main cell-wall amino acids were ornithine,alanine, glycine and glutamate. The cell wall peptidogly can sugars included glucose, rhamnose, galactose and mannose. The polar lipid present were DPG, PG, PE, and PIM. On the basis of DNA-DNA relatedness, phylogenetic position, complete genome sequence and physiological characteristics, strain P40-2^T can be differentiated from other species of the genus Cellulomonas with validly published names and thus represents a novel species, for which the name Cellulomonas taurus is proposed. The type strain is Cellulomonas taurus P40-2^T (= CGMCC No.1.17732^T).The acute toxicity test in mice showed that LD₅₀ of strain P40-2^T was rather high with 1.5 × 10¹¹ CFU/mouse, which indicated low pathogenicity. Drug susceptibility showed that strainP40-2^T was resistant to most antibiotics and only sensitive to six antibiotics. Strain P40-2^T contained a variety of hydrolytic enzymes including the ability to hydrolyze cellulose, β-glucan, chitin, xylan, and casein. Microbial flocculant MBF-P40 for sewage was prepared with strain P40-2^T, after strain P40-2^T was confirmed that had good flocculation effect. MBF-P40 was used to prepare flocculation rate of 99.40%. MBF-P40 treatmented sewage from eight different sources. Flocculation rate for pig farm wastewater was 96.07%, COD removal rate is 71.05%, ammonia nitrogen removal rate is 18.22%. The result shows that MBF-P40 has a good flocculation effect, and good prospect of development and application for wastewater treatment.

Complete Genome Sequence of Cellulomonas sp. JZ18, a Root Endophytic Bacterium Isolated from the Perennial Desert Tussock-Grass Panicum turgidum

Cellulomonas sp. JZ18 is a gram-positive, rod shaped bacterium that was previously isolated from the root endosphere of the perennial desert tussock-grass Panicum turgidum. Genome coverage of PacBio sequencing was approximately 199X. Genome assembly generated a single chromosome of 7,421,843 base pairs with a guanine-cytosine (GC) content of 75.60% with 3240 protein coding sequences, 361 pseudo genes, three ribosomal RNA operons, three non-coding RNAs and 45 transfer RNAs. Comparison of JZ18's genome with type strains from the same genus, using digital DNA-DNA hybridization and average nucleotide identity calculations, revealed that JZ18 might potentially belong to a new species. Functional analysis revealed the presence of genes that may complement previously observed biochemical and plant phenotypes. Furthermore, the presence of a number of enzymes could be of potential use in industrial processes as biocatalysts. Genome sequencing and analysis, coupled with comparative genomics, of endophytic bacteria for their potential plant growth promoting activities under different soil conditions will accelerate the knowledge and applications of biostimulants in sustainable agriculture.