Identification and differentiation of species and strains of Arthrobacter and Microbacterium barkeri isolated from smear cheeses with Amplified Ribosmal DNA Restriction Analysis (ARDRA) and pulsed field gel electrophoresis (PFGE)

Bioactivity of Microbacterium barkeri (LMA4) In Vitro and Candidate Gene Annotation In Silico

Actinomycetes are considered a never-ending treasure trove of biometabolites, which always fascinated researchers. However, to combat with newly emerging bacterial strains, the search for novel or analogs of existing therapeutic agents is recommended. In this context, this research work was carried out to search for a biopotent Actinomycetal strain grown in untapped soil, near the Hirakud dam. This Gram-positive bacteria was subjected to screening for its bioactivity against the medically important bacteria, isolated from local hospital sample using "co-culture" method, following both qualitative and quantitative assays. Further, the 16 s rRNA sequencing, BLASTn analysis, and GC% calculation were carried out. Based upon its bioactivity, a prediction-based genomics work was pursued, considering the gene sequence deposited in public domain. The reverse translation, elution of protein structural file, and the putative protein were predicted. The strain was identified as Microbacterium barkeri, with 54.1% GC content. From Gene Ontology term annotation, it was predicted that the α/β hydrolase fold of hydrolase protein could have been responsible for antibiotic/biometabolite synthesis, in silico. The in vitro-based sequence (from Whole Genome Sequence data) had inferred that there was elution of alpha/beta hydrolase fold, substantiated with conserved domain analysis, ORF finding more over Gene Ontology (GO) terminology annotations. The GO annotations had suggested that the protein had been produced in response to a bacteria, under the influence of external stimuli more so in stress.

Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections

INTRODUCTION

Cystic fibrosis (CF) airways are colonized by a polymicrobial community of organisms, termed the CF microbiota. We sought to define the microbial constituents of the home environment of individuals with CF and determine if it may serve as a latent reservoir for infection.

METHODS

Six patients with newly identified CF pathogens were included. An investigator collected repeat sputum and multiple environmental samples from their homes. Bacteria were cultured under both aerobic and anaerobic conditions. Morphologically distinct colonies were selected, purified and identified to the genus and species level through 16S rRNA gene sequencing. When concordant organisms were identified in sputum and environment, pulsed-field gel electrophoresis (PFGE) was performed to determine relatedness. Culture-independent bacterial profiling of each sample was carried out by Illumina sequencing of the V3 region of the 16s RNA gene.

RESULTS

New respiratory pathogens prompting investigation included: Mycobacterium abscessus(2), Stenotrophomonas maltophilia(3), Pseudomonas aeruginosa(3), Pseudomonas fluorescens(1), Nocardia spp.(1), and Achromobacter xylosoxidans(1). A median 25 organisms/patient were cultured from sputum. A median 125 organisms/home were cultured from environmental sites. Several organisms commonly found in the CF lung microbiome were identified within the home environments of these patients. Concordant species included members of the following genera: Brevibacterium(1), Microbacterium(1), Staphylococcus(3), Stenotrophomonas(2), Streptococcus(2), Sphingomonas(1), and Pseudomonas(4). PFGE confirmed related strains (one episode each of Sphinogomonas and P. aeruginosa) from the environment and airways were identified in two patients. Culture-independent assessment confirmed that many organisms were not identified using culture-dependent techniques.

CONCLUSIONS

Members of the CF microbiota can be found as constituents of the home environment in individuals with CF. While the majority of isolates from the home environment were not genetically related to those isolated from the lower airways of individuals with CF suggesting alternate sources of infection were more common, a few genetically related isolates were indeed identified. As such, the home environment may rarely serve as either the source of infection or a persistent reservoir for re-infection after clearance.

Growth stimulation of Brevibacterium sp. by siderophores

AIMS

To assess which types of siderophores are typically produced by Brevibacterium and how siderophore production and utilization traits are distributed within this genus.

METHODS AND RESULTS

During co-cultivation experiments it was found that growth of B. linens Br5 was stimulated by B. linens NIZO B1410 by two orders of magnitude. The stimulation was caused by the production of hydroxamate siderophores by B. linens NIZO B1410 that enabled the siderophore-auxotrophic strain Br5 to grow faster under the applied iron-limited growth conditions. Different patterns of siderophore production and utilization were observed within the genus Brevibacterium. These patterns did not reflect the phylogenetic relations within the group as determined by partial 16S rDNA sequencing. Most Brevibacterium strains were found to utilize hydroxamate siderophores.

CONCLUSIONS

Brevibacteria can produce and utilize siderophores although certain strains within this genus are siderophore-auxotrophic.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is reported for the first time that brevibacteria produce and utilize siderophores. This knowledge can be utilized to stimulate growth of auxotrophic strains under certain conditions. Enhancing the growth rate of Brevibacterium is of importance for the application of this species, for example, for cheese manufacturing or for industrial production of enzymes or metabolites.

Molecular identification and differentiation of Brevibacterium species and strains

Amplified ribosomal DNA restriction enzyme analysis (ARDRA), pulsed field gel electrophoresis (PFGE) and ribotyping were used to differentiate among 24 strains of Brevibacterium linens, Brevibacterium casei and Brevibacterium epidermidis obtained from type culture collections or isolated from various smear ripened cheeses. ARDRA was applied to the 16S rDNA. B. linens was shown to be a quite heterogenic group with 2 to at least 4 copies of rrn operons per strain with aberrant nucleotide sequences. AccI gave genus specific restriction patterns and was used to separate Brevibacterium from Corynebacterium species. The expected species specificity of TaqI applied to B. linens type culture strains, but not to all strains isolated from cheese. By AvaI restriction, B. casei and B. linens were differentiated from B. epidermidis and the orange pigmented Arthrobacter casei, a new species of coryneform bacteria; by XmnI restriction, B. linens and B. epidermidis were differentiated from B. casei. One of 4 B. linens genotypes could not be distinguished from B. casei by this method. Here, the typical orange B. linens pigments were used for classification, which was confirmed by partial sequencing of the 16S rDNA.

Surface microflora of four smear-ripened cheeses

The microbial composition of smear-ripened cheeses is not very clear. A total of 194 bacterial isolates and 187 yeast isolates from the surfaces of four Irish farmhouse smear-ripened cheeses were identified at the midpoint of ripening using pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR, and 16S rRNA gene sequencing for identifying and typing the bacteria and Fourier transform infrared spectroscopy and mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) analysis for identifying and typing the yeast. The yeast microflora was very uniform, and Debaryomyces hansenii was the dominant species in the four cheeses. Yarrowia lipolytica was also isolated in low numbers from one cheese. The bacteria were highly diverse, and 14 different species, Corynebacterium casei, Corynebacterium variabile, Arthrobacter arilaitensis, Arthrobacter sp., Microbacterium gubbeenense, Agrococcus sp. nov., Brevibacterium linens, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus saprophyticus, Micrococcus luteus, Halomonas venusta, Vibrio sp., and Bacillus sp., were identified on the four cheeses. Each cheese had a more or less unique microflora with four to nine species on its surface. However, two bacteria, C. casei and A. arilaitensis, were found on each cheese. Diversity at the strain level was also observed, based on the different PFGE patterns and mtDNA RFLP profiles of the dominant bacterial and yeast species. None of the ripening cultures deliberately inoculated onto the surface were reisolated from the cheeses. This study confirms the importance of the adventitious, resident microflora in the ripening of smear cheeses.

Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov., novel coryneform species isolated from the surfaces of cheeses

Fourteen isolates of two different bacterial species isolated from the surface of smear-ripened cheeses were found to exhibit many characteristics of the genus Arthrobacter. The isolates were aerobic, Gram-positive, catalase-positive, non-spore-forming and non-motile. The cell-wall peptidoglycan contained lysine, alanine and glutamic acid. rrs sequence analysis indicated that the new isolates Re117T and Ca106T are closely related to the Arthrobacter nicotianae group and showed highest sequence similarity (>98 %) to Arthrobacter nicotianae and Arthrobacter protophormiae. However, DNA-DNA hybridization studies indicated that the strains represented two novel genomic species within the genus Arthrobacter and did not belong to A. nicotianae or A. protophormiae (<43 % DNA-DNA relatedness). On the basis of the phylogenetic and phenotypic distinctiveness of the new isolates, these bacteria should be classified as two novel Arthrobacter species, for which the names Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov. are proposed. Type strains have been deposited in culture collections as Arthrobacter bergerei Ca106T (=CIP 108036T=DSM 16367T) and Arthrobacter arilaitensis Re117T (=CIP 108037T=DSM 16368T).