In vitro evaluation of methicillin-resistant and methicillin-sensitive Staphylococcus aureus susceptibility to Saudi honeys.

BACKGROUND: Honey has been increasingly recognized as a potential therapeutic agent for treatment of wound infections. There is an urgent need for assessment and evaluation of the antibacterial properties against wound pathogens of honeys that have not yet been tested. METHODS: Ten Saudi honeys collected from different geographical locations were screened initially for their antibacterial potential against methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA) by the agar well diffusion method. Manuka honey (UMF-12) was used for comparison. Of the tested honeys, the honey that exhibited the greatest antibacterial activity in the agar well diffusion assay was further evaluated for its minimum inhibitory concentration (MIC) against ten MRSA clinical isolates and three American Type Culture Collection (ATCC) reference strains by the microbroth dilution method. RESULTS: Locally produced honeys exhibited variable antibacterial activity against the tested isolates in the agar well diffusion assay. They were unable to exhibit antibacterial activity against MSSA and MRSA at 25% dilutions (w/v) in catalase solution. However, Sumra and Talha honeys showed a zone of inhibition at 50% dilutions (w/v) in catalase solution. This finding means that both honeys possess weak non-peroxide-based antibacterial activity. Moreover, Sumra honey showed a larger inhibition zone at 50 and 25% dilutions (w/v) in distilled water than Manuka honey against both MSSA and MRSA. This result demonstrates that Sumra honey has more hydrogen peroxide-related antibacterial activity or total antibacterial activity than Manuka honey. In addition, MIC results obtained through a microbroth dilution assay showed that Sumra honey inhibited the growth of all MRSA clinical isolates (n = 10) and reference strains [MRSA (ATCC 43300) and MSSA (ATCC 29213)] at lower concentrations (12.0% v/v) than those required for Manuka honey-mediated inhibition (14.0% v/v). This result means that Sumra honey has more peroxide or synergistic antibacterial activity than Manuka honey. An equivalent MIC (15.0% v/v) was observed for E. coli (ATCC 25922) between Manuka honey and Sumra honey. CONCLUSIONS: Sumra honey may be used as an alternative therapeutic agent for infected wounds and burns, where additional hydrogen peroxide-related antibacterial activity is needed. In the future, the physiochemical characteristics of Sumra honey may be evaluated and standardized.

Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut.

As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.

Infectious Agents and Neurodegenerative Diseases: Exploring the Links.

Recent studies have shown that bacterial and viral infections are risk factors for various neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS), Multiple Sclerosis (MS), Alzheimer's disease (AD), and Lyme disease (LD). However, it is still controversial how the infections play a role in neurological diseases progression. Infections in central nervous system may lead multiple damages in infected and neighboring cells. The infection leads to the activation of inflammatory processes and host immune responses, which acts as defense mechanism and also causes damage to the host neuronal functions and viability. Several bacterial and viral pathogens have been reported for neurodegeneration, such as the production and deposit of misfolded protein aggregates, oxidative stress, deficient autophagic processes, synaptopathies and neuronal death. These effects may act in combination with other factors, like aging, metabolic diseases and the genetic makeup of the host. We will focus in this review on the possible link between neurodegeneration and infections particularly Chlamydophila pneumoniae, Borrelia burgdorferi, Mycoplasma etc.

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov.

Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono-genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T, (= CSUR P1091=DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. The strain S5T was a Gram-positive, strictly aerobic rod, which was motile by a polar flagellum, spore-forming, and exhibited catalase and oxidase activities. It grows optimally at 37°C, with a pH of 7.5 and 10% of NaCl. 16S rRNA gene-based identification revealed that strain S5T has 98.6% 16S rRNA sequence similarity with the reference O. oncorhynchi, phylogenetically the closest validated Oceanobacillus species. Here, we further describe the phenotypic characteristics of this organism and its complete genome sequence and annotation. The 5,388,285 bp long genome exhibits a G+C content of 37.24% and contains 5109 protein-coding genes and 198 RNA genes. Based on the characteristics reported here, we propose classifying this novel bacterium as representative of a new species belonging to the genus Oceanobacillus, Oceanobacillus jeddahense sp. nov. In a broader context, it is noteworthy that halophilic bacteria have long been overlooked in the human gut, and their role in human health and disease has not yet been investigated. This study thus further underscores the usefulness of the culturomics approach exploring the bacterial diversity of the gut.

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov.

Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.

Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut.

Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus picturae, strain S1(T), whose genome is described here, from a stool sample collected from a 25-year-old Saoudian healthy individual. We used a slightly modified standard culture medium adding 100 g/L of NaCl. We provide a short description of this strain including its MALDI-TOF spectrum, the main identification tool currently used in clinical microbiology. The 3,675,175 bp long genome exhibits a G + C content of 39.15 % and contains 3666 protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb versus 3.83 Mb). The G + C content was higher compared with Oceanobacillus kimchii (respectively 39.15 % and 35.2 %). Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of Oceanobacillus picturae strain S1 isolated for the first time in a human, will be added to the 778 genome projects from the gastrointestinal tract listed by the international consortium Human Microbiome Project.

Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov.

Corynebacterium jeddahense sp. nov., strain JCB(T), is the type strain of Corynebacterium jeddahense sp. nov., a new species within the genus Corynebacterium. This strain, whose genome is described here, was isolated from fecal flora of a 24-year-old Saudi male suffering from morbid obesity. Corynebacterium jeddahense is a Gram-positive, facultative anaerobic, nonsporulating bacillus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation, and compare it to other member of the genus Corynebacterium. The 2,472,125 bp-long genome (1 chromosome but not plasmid) contains 2,359 protein-coding and 53 RNA genes, including 1 rRNA operon.