Arthrobacter nasiphocae sp. nov., from the common seal (Phoca vitulina)

Falsarthrobacter nasiphocae periprosthetic joint infection

We report the isolation of a rare Gram-positive coccobacillary bacterium from synovial fluids of a patient with periprosthetic joint infection on three occasions over an 8-month period. As routine microbiological methods were not able to identify the isolate definitely, sequence analyses of the bacterial 16S ribosomal RNA gene and whole genome were performed. Analysis of the bacterial 16S ribosomal RNA gene showed the highest similarity (98.1%) with that of Falsarthrobacter (previously known as Arthrobacter) nasiphocae, which was first isolated from the nasal cavities of common seals (Phoca vitulina). The genome size of the strain (designated as UM1) is 2.4 Mb. With a high G+C content (70.4 mol%), strain UM1 is phylogenetically most closely related to F. nasiphocae based on whole genome analysis. Strain UM1 was susceptible to vancomycin, linezolid, trimethoprim-sulfamethoxazole, doxycycline, and intermediate to penicillin and ciprofloxacin. Ceftriaxone resistance was noted. The patient who was also on hemodialysis for his end stage kidney disease died approximately 3 weeks following implant removal and fusion with an external fixator. This study describes the first isolation of F. nasiphocae from human clinical samples. The use of emerging technologies has supported more definitive etiological diagnosis associated with rarely encountered organisms in periprosthetic joint infection.

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.

Atypical Multibacterial Granulomatous Myositis in a Horse: First Report in Italy

Infectious causes of myositis are reported relatively uncommonly in horses. Among them, bacterial causes include Streptococcus equi subsp. zooepidemicus, Actinobacillus equuli, Fusobacterium spp. Staphylococcus spp, and Corynebacterium pseudotuberculosis. Infection can be spread to muscles via haematogenous or extension from skin lesions. Parasitic myositis has also been documented. In this report, a 12 year-old Italian Quarter Horse mare presented with diffuse subcutaneous nodules and masses ranging from 2 × 3 to 5 × 20 cm in size, and adherent to subcutis and muscles that were first macroscopically and cytologically diagnosed as pyogranulomas. Subsequently, histological, molecular, bacteriological, and biochemical investigations were performed. All the data obtained allowed to diagnose a severe and diffuse multibacterial granulomatous myositis caused by Corynebacterium pseudotuberculosis and Corynebacterium amycolatum. Following the therapy and an initial disappearance of most of the lesions together with a general improvement of the mare, the clinical condition deteriorated, and new nodules appeared. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and PCR techniques revealed the presence of bacteria as Glutamicibacter creatinolyticus and Dietzia spp. To the authors’ knowledge, this case report represents the first description of multibacterial granulomatous myositis due to Corynebacterium pseudotuberculosis, Corynebacterium amycolatum, Glutamicibacter creatinolyticus, and Dietzia spp. in a horse reared in Italy.

The Fecal Metagenomics of Malayan Pangolins Identifies an Extensive Adaptation to Myrmecophagy

The characteristics of flora in the intestine of an animal, including the number and abundance of different microbial species and their functions, are closely related to the diets of the animal and affect the physical condition of the host. The Malayan pangolin (Manis javanica) is an endangered species that specializes in myrmecophagy. Analyzing the microbiome in the intestine of the pangolin is imperative to protect this species. By sequencing the metagenomes of the feces of four pangolins, we constructed a non-redundant catalog of 211,868 genes representing 1,811 metagenomic species. Taxonomic annotation revealed that Bacteroidetes (49.9%), Proteobacteria (32.2%), and Firmicutes (12.6%) are the three main phyla. The annotation of gene functions identified 5,044 genes from 88 different glycoside hydrolase (GH) families in the Carbohydrate-Active enZYmes database and 114 gene modules related to chitin-degrading enzymes, corresponding to the catalytic domains of GH18 family enzymes, containing chitinase genes of classes III and V in the dataset. Fourteen gene modules corresponded to the catalytic domains of GH19 family enzymes, containing chitinase genes of classes I, II, and IV. These genes were found in 37 species belonging to four phyla: Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Moreover, when the metabolic pathways of these genes were summarized, 41,711 genes were associated with 147 unique KEGG metabolic pathways, and these genes were assigned to two Gene Ontology terms: metabolic process and catalytic activity. We also found several species that likely play roles in the digestion of cellulose and may be able to degrade chitin, including Enterobacter cloacae, Lactococcus lactis, Chitinimonas koreensis, and Chitinophaga pinensis. In addition, we identified some intestinal microflora and genes related to diseases in pangolins. Twenty-seven species were identified by STAMP analysis as differentially abundant in healthy and diseased animals: 20 species, including Cellulosilyticum lentocellum and Lactobacillus reuteri, were more abundant in healthy pangolins, while seven species, including Odoribacter splanchnicus, Marinilabilia salmonicolor, Xanthomonas citri, Xanthomonas vasicola, Oxalobacter formigenes, Prolixibacter bellariivorans, and Clostridium bolteae, were more abundant in diseased pangolins. These results will support the efforts to conserve pangolins.

Reclassification of Arthrobacter nasiphocae (Collins et al. 2002) as Falsarthrobacter nasiphocae gen. nov., comb. nov

The original description of Arthrobacter nasiphocae M597/99/10^T demonstrated that it is distantly related to the type species of the genus Arthrobacter, Arthrobacter globiformis, and that this phylogenetic relationship is reflected by the distinct peptidoglycan type [Lys-Ala2-Gly2-3-Ala(Gly)] and the features of the quinone system, which is composed of menaquinones MK-9(H2) and MK-8(H2). Here, we report a re-evaluation of the taxonomic status of A. nasiphocae. Phylogenetically, it was observed to be only distantly related to the genus Arthrobacter and to the type species of related genera. Re-analysis confirmed the quinone system menaquinones MK-9(H2) and MK-8(H2) in A. nasiphocae. Analysis of cell polar lipids showed a profile consisting of the predominant lipids diphosphatidylglycerol, phosphatidylglycerol, dimannosylglyceride, an unidentified phospholipid and an unidentified aminophosphoglycolipid, and several minor unidentified lipids. This profile clearly is different from that of Arthrobacter species. The cell fatty acid profile also showed characteristics that distinguished A. nasiphocae from Arthrobacter species. The phylogenetic distance of A. nasiphocae from any type species of genera within the family Micrococcaceae and the distinct chemotaxonomic traits warrant the reclassification of A. nasiphocae within a novel genus, for which we propose the name Falsarthrobacter nasiphocae gen. nov., comb. nov. The type strain is M597/99/10^T (=CCUG 42953^T=CIP 107054^T=DSM 13988^T=JCM 11677^T).

Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus

In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed, namely Glutamicibacter gen. nov. (nine species), Paeniglutamicibacter gen. nov. (six species), Pseudoglutamicibacter gen. nov. (two species), Paenarthrobacter gen. nov. (six species) and Pseudarthrobacter gen. nov. (ten species).

Isolation and characterization of vB_ArS-ArV2 - first Arthrobacter sp. infecting bacteriophage with completely sequenced genome

This is the first report on a complete genome sequence and biological characterization of the phage that infects Arthrobacter. A novel virus vB_ArS-ArV2 (ArV2) was isolated from soil using Arthrobacter sp. 68b strain for phage propagation. Based on transmission electron microscopy, ArV2 belongs to the family Siphoviridae and has an isometric head (∼63 nm in diameter) with a non-contractile flexible tail (∼194×10 nm) and six short tail fibers. ArV2 possesses a linear, double-stranded DNA genome (37,372 bp) with a G+C content of 62.73%. The genome contains 68 ORFs yet encodes no tRNA genes. A total of 28 ArV2 ORFs have no known functions and lack any reliable database matches. Proteomic analysis led to the experimental identification of 14 virion proteins, including 9 that were predicted by bioinformatics approaches. Comparative phylogenetic analysis, based on the amino acid sequence alignment of conserved proteins, set ArV2 apart from other siphoviruses. The data presented here will help to advance our understanding of Arthrobacter phage population and will extend our knowledge about the interaction between this particular host and its phages.

Draft Genome Sequence of Arthrobacter crystallopoietes Strain BAB-32, Revealing Genes for Bioremediation

Arthrobacter crystallopoietes strain BAB-32, a Gram-positive obligate aerobic actinobacterium having potential application in bioremediation and bioreduction of a few metals, was isolated from rhizosphere soil of Gandhinagar, Gujarat, India. The draft genome (4.3 Mb) of the strain revealed a few vital gene clusters involved in the metabolism of aromatic compounds, zinc, and sulfur.

Arthrobacter equi sp. nov., isolated from veterinary clinical material

A Gram-positive-staining, catalase-positive, non-spore-forming, rod-shaped bacterium, strain IMMIB L-1606(T), isolated from genital swabs of a horse, was characterized using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the organism was related to members of the genus Arthrobacter, displaying sequence similarities of 93.5-99.1 % with the type strains of recognized species of the genus. Cell-wall analysis revealed peptidoglycan type A3α L-Lys-L-Ser-L-Thr-L-Ala. DNA-DNA hybridization data and biochemical characterization of strain IMMIB L-1606(T) enabled the isolate to be differentiated genotypically and phenotypically from phylogenetically closely related species of the genus Arthrobacter. Therefore, it is concluded that strain IMMIB L-1606(T) represents a novel species of the genus Arthrobacter, for which the name Arthrobacter equi sp. nov. is proposed. The type strain of Arthrobacter equi sp. nov. is IMMIB L-1606(T) ( = DSM 23395(T) = CCUG 59597(T)).

Arthrobacter antarcticus sp. nov., isolated from an Antarctic marine sediment

A bacterial strain, SPC26(T), was isolated from a sediment sample of the Southern Ocean off Antarctica. The strain was Gram-staining- and catalase-positive and contained lysine and alanine in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C₁₅:₀ (54.92 %), iso-C₁₅:₀ (11.47 %), anteiso-C₁₇:₀ (6.48 %) and anteiso-C₁₅:₁ (6.38 %) and the major menaquinones were MK-8, MK-9 and MK-10. The major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The G+C content was 68 ± 0.5 mol%. Based on 16S rRNA gene sequence similarities, the nearest phylogenetic neighbours of strain SPC26(T) were identified as Arthrobacter gangotriensis Lz1y(T) (98.8 %), A. sulfureus DSM 20167(T) (98.6 %), A. psychrophenolicus DSM 15454(T) (97.9 %) and A. kerguelensis KGN15(T) (97.5). With these strains, strain SPC26(T) exhibited DNA-DNA relatedness values of 36, 21, 12 and 10 %, respectively. Therefore, on the basis of 16S rRNA gene sequence comparisons, phylogenetic analysis, phenotypic characteristics and DNA-DNA relatedness, it is proposed that strain SPC26(T) represents a novel species of Arthrobacter, for which the name Arthrobacter antarcticus sp. nov. is proposed, with strain SPC26(T) (=LMG 24542(T) =NCCB 100228(T)) as the type strain.

Xylose utilization and short-chain fatty acid production by selected components of the intestinal microflora of a rodent pollinator (Aethomys namaquensis)

Namaqua rock mice (Aethomys namaquensis) consume nectar xylose when visiting Protea flowers. Whole-animal metabolism studies suggest that the gastrointestinal microflora plays an important role in xylose metabolism in A. namaquensis. We collected caecal contents under anaerobic conditions, cultured caecal microflora both aerobically and anaerobically, and assessed caecal microbial xylose utilization using a (14)C-xylose incubation assay. All four mice sampled hosted culturable caecal micro-organisms that tested positive for xylose utilization. These were classified by 16S rRNA based taxonomy as: Bacillus subtilis, Bacillus pumilus, Bacillus licheniformis, Shigella boydii, Arthrobacter sp. and members of the fungal genera Aspergillus and Penicillium. Cultures of these isolates were then analyzed by gas chromatography to determine the types and quantities of short-chain fatty acids produced by xylose fermentation. These results are discussed in the context of other studies of gut microflora in vertebrates.