Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).

Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds

Diversity of culturable moderately halophilic and halotolerant bacteria in a marsh and two salterns a protected ecosystem of Lower Loukkos (Morocco)

To study the biodiversity of halophilic bacteria in a protected wetland located in Loukkos (Northwest, Morocco), a total of 124 strains were recovered from sediment samples from a marsh and salterns. 120 isolates (98%) were found to be moderately halophilic bacteria; growing in salt ranges of 0.5 to 20%. Of 124 isolates, 102 were Gram-positive while 22 were Gram negative. All isolates were identified based on 16S rRNA gene phylogenetic analysis and characterized phenotypically and by screening for extracellular hydrolytic enzymes. The Gram-positive isolates were dominated by the genus Bacillus (89%) and the others were assigned to Jeotgalibacillus, Planococcus, Staphylococcus and Thalassobacillus. The Gram negative isolates were dominated by the genus Vibrio (41%) and the others were assigned to Halomonas, Psychrobacter, Marinobacterium, Pseudoalteromonas, Salinivibrio and Photobacterium. The growth of strains obtained under different physico-chemical conditions and the screening for hydrolytic enzymes showed a high diversity even within the same species

The Bulk and The Tail of Minimal Absent Words in Genome Sequences

Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the novel concept of a core of a minimal absent word, which are sequences present in the genome and closest to a given MAW. We show that in bacteria and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs (rRNAs). We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.Comment: Supplemental Information to the paper is available as ancillary fil

EVALUATION OF ANTIBIOTIC RESISTANCE PROFILES OF HALOBACTERIA ISOLATED FROM THE FOOD CHAIN

L’insorgenza e la diffusione dell’antibiotico resistenza sta diventando un problema a livello mondiale. Molti sono gli ambienti in cui può avvenire tale diffusione, ma una delle principali vie di trasmissione passa attraverso la catena alimentare. Infatti, l’utilizzo di sostanze antimicrobiche è largamente diffuso negli allevamenti di animali ad uso alimentare e in agricoltura. In particolare, negli allevamenti gli antibiotici non solo vengono usati per trattare eventuali patologie, ma anche come profilassi e come promotori di crescita. Di conseguenza, questo uso a volte sconsiderato ha portato all’insorgenza di batteri resistenti a tali sostanze. Un ruolo fondamentale nella trasmissione e diffusione di tali resistenze a livello alimentare è svolto da batteri non patogeni che sono parte del naturale microbiota degli alimenti. Questi microorganismi infatti, pur non essendo essi stessi nocivi per l’uomo, possono fungere da reservoir di antibiotico resistenze per eventuali batteri patogeni. I batteri che generalmente svolgono questo ruolo sono i batteri lattici. Per questo motivo molto importante è stato identificare e studiare l’antibiotico resistenza anche di tali microorganismi. Negli ultimi anni, tuttavia, c’è stato un crescente interesse per un’altra classe di microorganismi, chiamata Haloarchaea o alobatteri o archaea alofili, poiché la loro presenza è stata rilevata in alimenti particolarmente salati. Dal momento che in letteratura ci sono pochi lavori che studiano i profili di antibiotico resistenza di tali microorganismi e, comunque, tali profili non sono stati studiati su un numero significativo di microorganismi appartenenti alla stessa specie, il presente lavoro di tesi è volto a definire il profilo di antibiotico resistenza del capostipite degli archaea alofili, che è l’Halobacterium salinarum, verificare se ci sono ceppi che presentano antibiotico resistenze e controllare se tali resistenze possono essere trasferite a batteri patogeni.Antimicrobial resistance is now widely acknowledged as a major global public health challenge. There are many environments through which the transmission and diffusion of antibiotic resistance could happen, but one of the main routes of transmission is the food chain. As a matter of fact, antibiotic use is widely spread in animal husbandry and in agriculture. In particular, in animal husbandry antimicrobials have been used both for therapeutic reasons and as growth promoters. As a consequence, a selective pressure on pathogenic and commensal bacteria of animal origin has been exerted during the time, leading to the onset of microorganisms resistant to such compounds. A pivotal role in the spread in the food chain of antibiotic resistance has been played by non-pathogenic bacteria present in food. These microorganisms are not harmful for humans, but they could represent a reservoir of antibiotic resistance for foodborne pathogenic bacteria. Usually lactic acid bacteria play this role, since they are present in all fermented food. For this reason, the antibiotic resistance profile of lactic acid bacteria has been assessed. In recent years, another class of microorganisms called halophilic archaea have raised an increasing scientific interest, since they have been found in the human intestinal mucosa as well as in foods such as salted codfish and fermented Asiatic seafood. As a few papers have studied the antibiotic resistance profiles of halophilic archaea, and the only present do not consider a statistically significant number of microorganisms belonging to the same species, the aim of the present work is to define the antibiotic resistance profile of the major exponent of halophilic archaea, named Halobacterium salinarum, and consequently to verify if some strains present antibiotic resistances and if they can transfer these resistances to bacteria present in the food chain

Draft genome sequence of Kocuria sp. strain UCD-OTCP (phylum Actinobacteria)

© 2013 Coil et al. Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds

Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis

Korean Fermented Foods and Mediterranean Diet: a review of the literature

openMediterranean diet is a well-known healthy diet based on a food pyramid constituted by seven steps (from the bottom to the top, step one water, step two fruits, vegetables, cereals, olive oil, step three nuts, seeds, herbs, wine, step four dairy, step five fish, eggs, white meat, legumes, step six red meat and processed meat, and step seven sweets) that incorporate lifestyle and cultural elements that makes it unique. Korean diet, instead, is a less known healthy diet characterized by a high consumption of plant-derived products and moderate intake of animal-derived food. It consists of grains (mainly rice), seaweed, fish, vegetables, and meat in moderation, therefore it has high carbohydrate and low-fat contents. Korean diet is based on the huge consumption of fermented foods such as Gangjang, Doenjang, Cheonggukjang, Gochujang, Jeotgal, and Kimchi. Fermented foods are worldwide recognized as health promoter for their ability in prevent and ameliorate chronic diseases such as obesity, cardiovascular diseases, diabetes, cancer, metabolic syndrome, neurodegenerative diseases, hypertension, and osteoporosis while having antioxidant and anti-inflammatory properties. In this context, my thesis reports a review of the literature on Korean fermented foods and analyzes the possible positive effect of a combination between Korean fermented foods and Mediterranean diet. Findings of this work underline the fundamental health benefits of Korean fermented food that, from the point of view of the enhancement of health benefits and sensorial characteristics, could indeed be an important addition to Mediterranean diet. Further research, however, is needed to evaluate the acceptability of Korean fermented foods among Mediterranean’s inhabitants and producers.Mediterranean diet is a well-known healthy diet based on a food pyramid constituted by seven steps (from the bottom to the top, step one water, step two fruits, vegetables, cereals, olive oil, step three nuts, seeds, herbs, wine, step four dairy, step five fish, eggs, white meat, legumes, step six red meat and processed meat, and step seven sweets) that incorporate lifestyle and cultural elements that makes it unique. Korean diet, instead, is a less known healthy diet characterized by a high consumption of plant-derived products and moderate intake of animal-derived food. It consists of grains (mainly rice), seaweed, fish, vegetables, and meat in moderation, therefore it has high carbohydrate and low-fat contents. Korean diet is based on the huge consumption of fermented foods such as Gangjang, Doenjang, Cheonggukjang, Gochujang, Jeotgal, and Kimchi. Fermented foods are worldwide recognized as health promoter for their ability in prevent and ameliorate chronic diseases such as obesity, cardiovascular diseases, diabetes, cancer, metabolic syndrome, neurodegenerative diseases, hypertension, and osteoporosis while having antioxidant and anti-inflammatory properties. In this context, my thesis reports a review of the literature on Korean fermented foods and analyzes the possible positive effect of a combination between Korean fermented foods and Mediterranean diet. Findings of this work underline the fundamental health benefits of Korean fermented food that, from the point of view of the enhancement of health benefits and sensorial characteristics, could indeed be an important addition to Mediterranean diet. Further research, however, is needed to evaluate the acceptability of Korean fermented foods among Mediterranean’s inhabitants and producers

Antibacterial activities of bacteria isolated from the marine sponges Isodictya compressa and Higginsia bidentifera collected from Algoa Bay, South Africa

Due to the rise inmulti-drug resistant pathogens and other diseases, there is renewed interest in marine sponge endosymbionts as a rich source of natural products (NPs). The South African marine environment is rich in marine biota that remains largely unexplored and may represent an important source for the discovery of novel NPs.We first investigated the bacterial diversity associated with five South African marine sponges, whose microbial populations had not previously been investigated, and select the two sponges (Isodictya compressa and Higginsia bidentifera) with highest species richness to culture bacteria. By employing 33 different growth conditions 415 sponge-associated bacterial isolates were cultured and screened for antibacterial activity. Thirty-five isolates showed antibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implying that some of the bioactive compounds could be novel. Genome sequencing of two of these isolates confirmed that they harbour uncharacterized biosynthetic pathways that may encode novel chemical structures.IS

Complexity and dynamics of the winemaking bacterial communities in berries, musts, and wines from apulian grape cultivars through time and space

Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.Peer ReviewedPostprint (published version