Brachybacterium paraconglomeratum Endophthalmitis Postcataract Operation

Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces

Brachybacterium species have been identified in various ecological niches and belong to the family Dermabacteriaceae within the phylum Actinobacteria. In this study, we isolated a novel Brachybacterium equifaecis JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other Brachybacterium strains. Moreover, comparative genomic analysis using publicly available Brachybacterium genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5-82.5%), average amino acid identity (66.7-75.8%), and in silico DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of Brachybacterium species. Most of the Brachybacterium strains displayed high oxygen (K m(app) =1.6-24.2 µM) and glucose (K m(app) =0.73-1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of Brachybacterium species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of Brachybacterium species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation. IMPORTANCE Basic physiological and genomic properties of most of the Brachybacterium isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel Brachybacterium strain through physiological and comparative genomic analysis. In addition, we presented the first report examining Brachybacterium kinetics, indicating that all strains of Brachybacterium, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.

Comparison of automatic methods MALDI-TOF, VITEK2 and manual methods for the identification of intestinal microbial communities on the example of samples from alpacas (Vicugna pacos)

Introduction

Universally, in microbiological diagnostics the detection of live bacteria is essential. Rapid identification of pathogens enables appropriate remedial measures to be taken. The identification of many bacteria simultaneously facilitates the determination of the characteristics of the accompanying microbiota and/or the microbiological complexity of a given environment.

Material and Methods

The effectiveness of the VITEK2 Compact automated microbial identification system and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), analytical profile index (API) and Remel RapID tests were compared in identification of bacteria isolated from the alpaca gastrointestinal tract.

Results

Most isolates were Gram-positive, such as Bacillus cereus, Bacillus flexus, Bacillus licheniformis, Bacillus pumilus and Bacillus subtilis; Enterococcus faecium, Enterococcus gallinarum, Enterococcus hirae and Enterococcus casseliflavus; Staphylococcus aureus, Staphylococcus equorum, Staphylococcus lentus, Staphylococcus pseudintermedius and Staphylococcus sciuri; Paenibacillus amylolyticus; Cellulosimicrobium cellulans; Leuconostoc mesenteroides; Clostridium perfringens; Corynebacterium stationis, Corynebacterium xerosis, and Corynebacterium diphtheriae (the last only isolated manually by API Coryne and the VITEK2 system and Corynebacteria (CBC) card). Corynebacterium diphtheriae was misidentified by MALDI-TOF MS as Candida lipolytica (currently Yarrowia lipolytica). Gram-positive and Gram-variable Micrococcus luteus were also isolated. Gram-negative Enterobacter cloacae, Enterobacter gergoviae, Enterobacter hormaechei and Enterobacter ludwigii; E. coli; Klebsiella pneumoniae subsp. pneumoniae; Citrobacter braakii and Citrobacter freundii; Serratia liquefaciens, Serratia odorifera and Serratia marcescens; Morganella morganii subsp. morganii; Providencia alcalifaciens; Pseudomonas aeruginosa; Stenotrophomonas maltophilia; Moraxella osloensis; and Ochrobactrum intermedium were also found. The yeasts Candida albicans, Candida haemulonii and Candida ciferrii were also present.

Conclusion

MALDI-TOF MS enabled the identification of pathogens and opportunistic pathogens from the alpaca gut which may represent a high risk to human and animal health.

The abundance of the potential pathogen Staphylococcus hominis in the air microbiome in a dental clinic and its susceptibility to far‐UVC light

The dental clinic air microbiome incorporates microbes from the oral cavity and upper respiratory tract (URT). This study aimed to establish a reliable methodology for air sampling in a dental clinic setting and quantify the abundance of culturable mesophilic aerobic bacteria present in these samples using regression modeling. Staphylococcus hominis, a potentially pathogenic bacterium typically found in the human oropharynx and URT, was consistently isolated. S. hominis was the most abundant species of aerobic bacteria (22%–24%) and comprised 60%–80% of all Staphylococcus spp. The study also assessed the susceptibility of S. hominis to 222 nm‐far‐UVC light in laboratory experiments, which showed an exponential surface inactivation constant of k = 0.475 cm²/mJ. This constant is a critical parameter for future on‐site use of far‐UVC light as a technique for reducing pathogenic bacterial load in dental clinics.

Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers

Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18–30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.