Search Results (34)

Genome-based discovery provides a powerful approach for identifying bioactive natural products. In this study, Streptomyces sp. PSU-S4-23 was isolated from soil collected in southern Thailand. Genome analysis revealed a nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster highly similar to the reference actinomycin D cluster, including canonical NRPS genes and a cytochrome P450 associated with oxidative tailoring. Genomic comparison indicated that this strain is distinct from its closest relative S. caeni CGMCC 4.7426^T with ANIb and dDDH values below the species delineation thresholds. In agar diffusion assays, the crude extract exhibited antibacterial activity against Staphylococcus aureus (MSSA and MRSA), Bacillus subtilis, Bacillus cereus, Enterococcus faecalis, Staphylococcus epidermidis, as well as inhibition of Pseudomonas aeruginosa and Acinetobacter baumannii. LC–MS/MS profiling of the crude ethyl-acetate extract was performed. GNPS feature-based molecular networking revealed ions corresponding to actinomycin X₂ (m/z 1269.6), D (m/z 1255.6), and I (m/z 1271.6), confirming production of multiple actinomycin analogs. These findings highlight Streptomyces sp. PSU-S4-23 as a promising actinomycin-producing strain with potential relevance to antibiotic discovery. Full article

In this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) nuclear ribosomal RNA (rRNA) regions. As this was the second species to be reported in this genus, we sequenced the genome of this species to increase our knowledge about the possible applicability of this genus to various industries. Its genome length was found to be 35.01 Mb, harboring 7870 protein-coding genes as per Augustus and 8101 genes using GeMoMa. Many genes were annotated using the Clusters of Orthologous Groups (COGs) database, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Swiss-Prot, NCBI non-redundant nucleotide sequences (NTs), and NCBI non-redundant protein sequences (NRs). The number of repeating sequences was predicted using Proteinmask and RepeatMasker; tRNA were detected using tRNAscan and snRNA were predicted using rfam_scan. The genome was also annotated using the Pathogen–Host Interactions Database (PHI-base) and AntiSMASH. To confirm the evolutionary history, average nucleotide identity (ANIb), phylogeny based on orthologous proteins, and single nucleotide polymorphisms (SNPs) were carried out. Metabolic profiling of the methanolic extract of dried biomass and ethyl acetate extract of the filtrate revealed a variety of compounds of great importance in the pharmaceutical and cosmetic industry. The characterization and genomic analysis of the newly discovered species Alanomyces manoharacharyi highlights its potential applicability across multiple industries, particularly in pharmaceuticals and cosmetics due to its diverse secondary metabolites and unique genetic features it possesses. Full article

This study describes two cases of bacteraemia sustained by a new putative Pannonibacter species isolated at the U.O.C. of Microbiology and Virology of the Policlinico of Bari (Bari, Italy) from the blood cultures of two patients admitted to the Paediatric Oncohaematology Unit. Pannonibacter spp. is an environmental Gram-negative bacterium not commonly associated with nosocomial infections. Species identification was performed using Sanger sequencing of the 16S rRNA gene and Whole-Genome Sequencing (WGS) for both strains. Genomic analyses for the two isolates, BLAST similarity search, and phylogeny for the 16S rDNA sequences lead to an assignment to the species Pannonibacter phragmitetus. However, by performing ANIb, ANIm, tetranucleotide correlation, and DNA-DNA digital hybridization, analyses of the two draft genomes showed that they were very different from those of the species P. phragmitetus. MALDI-TOF analysis, assessment of antimicrobial susceptibility by E-test method, and Analytical Profile Index (API) tests were also performed. This result highlights how environmental bacterial species can easily adapt to the human host and, especially in nosocomial environments, also gain pathogenic potential through antimicrobial resistance. Full article

One of the causal agents of bacterial canker is Pseudomonas amygdali pv. morsprunorum—Pam (formerly Pseudomonas syringae pv. morsprunorum). Recently detected in Chile, Pam is known to cause lesions in the aerial parts of the plant, followed by more severe symptoms such as cankers and gummosis in the later stages of the disease. This study presents the design of PCR and LAMP detection methods for the specific and sensitive identification of Pseudomonas amygdali pv. morsprunorum (Pam) from cherry trees. Twelve Pseudomonas isolates were collected, sequenced, and later characterized by Multi-locus Sequence Analysis (MLSA) and Average Nucleotide Identity by blast (ANIb). Three of them (11116B2, S1 Pam, and S2 Pam) were identified as Pseudomonas amygdali pv. morsprunorum and were used to find specific genes through RAST server, by comparing their genome with that of other Pseudomonas, including isolates from other Pam strains. The effector gene HopAU1 was selected for the design of primers to be used for both techniques, evaluating sensitivity and specificity, and the ability to detect Pam directly from plant tissues. While the PCR detection limit was 100 pg of purified bacterial DNA per reaction, the LAMP assays were able to detect up to 1 fg of purified DNA per reaction. Similar results were observed using plant tissues, LAMP being more sensitive than PCR, including when using DNA extracted from infected plant tissues. Both detection methods were tested in the presence of 30 other bacterial genera, with LAMP being more sensitive than PCR. Full article

The multiple roles of polyunsaturated fatty acids (PUFA) in growth and general health are well documented. However, available intake data for the Spanish population are limited and lack gender and age considerations. Therefore, our goal was to assess dietary intake adequacy of omega-3 and omega-6 PUFA, their determinants and their major food sources among the Spanish population. Due to their influence on various beneficial functions attributed to omega-3 PUFA, combined intake adequacy with folic acid (FA), vitamin B₁₂ and choline was also assessed. Intake data were obtained from the ANIBES cross-sectional study on a representative sample of the Spanish population (9–75 years; n = 2009), where dietary intake was analysed with a three-day dietary record. Median intake of total omega-3 PUFA stood at 0.81 g/day (0.56–1.19 g/day), with α-linolenic acid (ALA) at 0.61 g/day (0.45–0.85 g/day), eicosapentaenoic acid (EPA) at 0.03 g/day (0.01–0.12 g/day) and docosahexaenoic acid (DHA) at 0.06 g/day (0.0–0.20 g/day). Accordingly, 65% of the Spanish population showed insufficient intakes for total omega-3 PUFA; 87% for ALA, and 83% for combined EPA and DHA. Inadequate intakes were significantly higher in children, adolescents, and younger women of childbearing age (18–30 years). In contrast, inadequacy due to excessive intakes was almost negligible. Regarding omega-6 PUFA, total intake was 10.1 g/day (7.0–14.0 g/day), 10.0 g/day (6.9–13.9 g/day) for linoleic acid (LA) and 0.08 g/day (0.05–0.13 g/day) for arachidonic acid (AA). Non-compliance due to either insufficient or excessive intakes of LA stood at around 5% of the sample, with the elderly showing significantly higher degrees of inadequacy due to insufficient intakes (10%; p ≤ 0.05). Median omega-6 to omega-3 ratio was 12:1, and significantly higher in men compared to women (p ≤ 0.05); in children, adolescents and adults compared to the elderly (p ≤ 0.05); and in younger women of childbearing age compared to the older group (31–45 years) (p ≤ 0.001). Oils and fats and meat and meat products were the main dietary sources for the essential fatty acids LA and ALA, respectively. Meat and meat products were as well the main providers of AA, while fish and shellfish were almost exclusively the only sources of EPA and DHA. However, main food sources identified showed important differences across age groups. Finally, the total combined degree of inadequacy observed for omega-3 PUFA, FA, vitamin B₁₂ and choline reached 21.3% of the ANIBES population. The observed degree of inadequacy of omega-3 PUFA intakes among the Spanish population makes it urgent to increase its consumption and to consider the need for supplementation. This should also be the main strategy for the optimization of the omega-6/omega-3 ratio, as the adequacy observed for omega-6 intakes is relatively acceptable. Additional improvement of the dietary intake of FA, vitamin B₁₂ and choline could contribute to the beneficial effects of omega-3 PUFA. Full article

Stutzerimonas is a recently proposed genus within the Pseudomonadaceae comprising strains in the formerly phylogenetic group of Pseudomonas stutzeri. At least sixteen named species have to be included in the genus, together with 22 genomovars of Stutzerimonas stutzeri. To clarify the taxonomy of Stutzerimonas, a core-genome phylogeny of 200 strains in the genus was inferred and monophyletic strains with average nucleotide identities (ANIb) with values equal to or higher than 95 were grouped in the same phylogenomic species. A total of 45 phylogenomic species within the genus Stutzerimonas were detected in the present study. Sixteen phylogenomic species correspond to already named species, although three of them are not yet validated and two are proposed in the present study. A synonymy was detected between P. kunmingensis and S. chloritidismutans, both members of phylogenomic species 3, with a prevalence of the S. chloritidismutans name. The correspondence of the phylogenomic species to the genome taxonomy database classification (GTDB taxonomy) is discussed. Combining phylogenomic and phenotypic data, two novel species are described (Stutzerimonas frequens and Stutzerimonas degradans) and two species descriptions are emended (Stutzerimonas perfectomarina and Stutzerimonas chloritidismutans). Full article

Growing evidence confirms choline as a critical perinatal nutrient. However, intake levels of choline and betaine among the Spanish fertile population remain unknown. Given their role in one-carbon metabolism with potential epigenetic effects, the aim of the present study was to evaluate the dietary intakes, their adequacy to existing guidelines and the main food sources together with other micronutrients involved in the methylation-methionine cycle (vitamin B₆, folates and vitamin B₁₂) in women of childbearing age. The ANIBES study, a cross-sectional study of a representative sample of women of childbearing age (18–45 years, n = 641) resident in Spain, was used. The sample was divided into younger women (18–30 years, n = 251) and older women (31–45 years, n = 390). Dietary intake was assessed by a three-day dietary record by using a tablet device. Total median intakes for the total sample were 303.9 mg/d for choline; 122.6 mg/d for betaine; 1.3 mg/d for vitamin B₆; 140.8 μg/d for folates, and 3.8 μg/d for vitamin B₁₂. The older subgroup showed significantly higher choline (p < 0.05), betaine (p < 0.001) and folates (p < 0.05) intakes than younger women. Main food sources for the whole sample were meat and meat products for choline (28.3%), vitamin B₆ (25.7%) and vitamin B₁₂ (22.8%); cereals and derivatives (79.9%) for betaine; vegetables (20.0%) for folates. Overall intake adequacy was only observed for vitamin B₁₂, with a very limited number of participants showing adequate intakes for all the other micronutrients. These results illustrate there is a relevant need to raise awareness about optimizing the status of the methionine cycle-related vitamins and cofactors in this potentially vulnerable population. Full article

Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. We present a first report on the enrichment and isolation of a methanotroph, strain BlB1, from the faeces of an Indian antelope (blackbuck). The 16S rRNA gene sequence of strain BlB1 showed the highest identity (98.40% identity) to Methylobacter marinus A45^T and Methylobacter luteus NCIMB 11914^T. Strain BlB1 showed coccoidal cells (1.5–2 µm in diameter), which formed chains or aggregates of 3–4 cells of light yellow-coloured colonies on agarose when incubated with methane in the gas phase. The draft genome of BlB1 (JADMKV01) is 4.87 Mbp in size, with a G + C content of 51.3%. The draft genome showed 27.4% digital DNA-DNA hybridization (DDH) and 83.07% average nucleotide identity (ANIb) values with that of its closest phylogenetic neighbour, Methylobacter marinus A45^T. Due to the lower values of DDH and ANIb with the nearest species, and <98.7% 16S rRNA gene sequence identity, we propose that strain BlB1 belongs to a novel species of Methylobacter. However, as the culture has to be maintained live and resisted cryopreservation, deposition in culture collections was not possible and hence we propose a Candidatus species name, ‘Ca. Methylobacter coli’ BlB1. ‘Ca. Methylobacter coli’ BlB1 would be the first described methanotroph from ruminants worldwide, with a sequenced draft genome. This strain could be used as a model for studies concerning methane mitigation from ruminants. Full article

Three novel Gram-positive, aerobic, chemoheterotrophic, motile, non-endospore-forming, orange-pigmented bacteria designated strains T13^T, T90^T and R8^T were isolated from the Tabernas Desert biocrust (Almería, Spain). Cells of the three strains were coccus-shaped and occurred singly, in pairs or clusters. The three strains were oxidase-negative and catalase-positive, and showed a mesophilic, neutrophilic and non-halophilic metabolism. Based on the 16S rRNA gene sequences, the closest neighbours of strains T13^T, T90^T and R8^T were Kineococcus aurantiacus IFO 15268^T, Kineococcus gypseus YIM 121300^T and Kineococcus radiotolerans SRS 30216^T (98.5%, 97.1% and 97.9% gene sequence similarity, respectively). The genomes were sequenced, and have been deposited in the GenBank/EMBL/DDBJ databases under the accession numbers JAAALL000000000, JAAALM000000000 and JAAALN000000000, respectively, for strains T13^T, T90^T and R8^T. The average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to three new species within the genus Kineococcus. The genomic G + C content of strains T13^T, T90^T and R8^T ranged from 75.1% to 76.3%. The predominant fatty acid of all three strains was anteiso-C_15:0. According to a polyphasic study, strains T13^T, T90^T and R8^T are representatives of three new species in the genus Kineococcus, for which names Kineococcus vitellinus sp. nov. (type strain T13^T = CECT 9936^T = DSM 110024^T), Kineococcus indalonis sp. nov. (type strain T90^T = CECT 9938^T = DSM 110026^T) and Kineococcus siccus sp. nov. (type strain R8^T = CECT 9937^T = DSM 110025^T) are proposed. Full article

Food waste is a major environmental issue that must be tackled in order to achieve a sustainable food supply chain. Currently, in Spain there are no studies that examine the amounts and sources of plate waste (PW) produced by both household and out-of-home consumption. The present study aims to provide this information from a representative sample from the Spanish population. A total of 2009 individuals aged 9–75 years, from the ANIBES study (“anthropometric data, macronutrients and micronutrients intake, practice of physical activity, socioeconomic data and lifestyles in Spain”), completed a three-day dietary record, collected by a tablet device. Photographs of all foods and beverages consumed both at home and outside were taken before and after meals. Median PW across the total population was 7.3 (0.0–37.3) g/day and was significantly higher in females than males (p < 0.05) and in children vs. adolescents, adults, and elderly (p < 0.01). Regarding meals, PW across all age groups was higher at lunch (40%), dinner (27%), and breakfast (11%). The highest PW was observed for bread (25%) main courses (16%), first and second courses (15%), vegetables and fruits (12%), ready-to-eat meals (10%), cereals and grains (10%), oils and fats (10%), pulses (10%), meat products (8%), sauces and condiments (8%), and starters (8%). Our results reinforce the need for new strategies to focus on reducing plate leftovers, which are crucial from a nutritional, economic, and environmental point of view. Additionally, this evidence is important for relying on more accurate information on actual intakes when using dietary surveys. Full article

Active commuting (AC) has been proposed as a great opportunity to increase physical activity level (PA) in children and adolescents. The aim of the present study is to determine the associations between AC (walk and cycle commuting) and non-AC (motor vehicle commuting) with PA levels, and with AC and sedentarism in Spanish children and adolescents. A representative Spanish sample of 424 children and adolescents (38% females) was involved in the ANIBES (Anthropometry, Dietary Intake and Lifestyle in Spain) Study in 2013. Data on the levels of AC, non-AC, PA, and sedentarism were obtained using the International Physical Activity Questionnaire for adolescents. Stepwise backward univariate generalized linear and linear regression models were performed. In girls, walking was associated with playground PA, moderate PA, and moderate to vigorous PA (MVPA) (β = 0.007, p < 0.05; both β = 0.007, p < 0.01), respectively. In boys, walking was associated with all PA levels (p < 0.05); while cycling was related to moderate PA and MVPA (both β = 0.007, p < 0.05). A negative significant association was observed between AC and time spent studying without Internet use in boys (β = −0.184, p < 0.05). Commuting by walking contributes to increased daily PA in both sexes, whereas cycling was only related to moderate PA and MVPA in boys. Sedentary behaviors are not related to AC, but studying without Internet use was negatively associated with AC in boys. Full article

Dietary habits amongst the Spanish population are currently a relevant cause for concern, as macronutrient profiles and micronutrient intakes seem to be inadequate and globally moving away from the traditional Mediterranean dietary pattern. However, recent food consumption patterns have not been fully assessed. In the present study, our aim was therefore to describe the current food consumption from the “anthropometric data, macronutrients and micronutrients intake, practice of physical activity, socioeconomic data and lifestyles in Spain” (ANIBES) study population by assessing data defined by age and gender. The ANIBES study is a cross-sectional study of a nationally representative sample of the Spanish population. A three-day dietary record was used to obtain information about food and beverage consumption. The sample comprised 2009 individuals aged 9–75 years, plus a boost sample for the youngest age groups (9–12, 13–17, and 18–24 years, n = 200 per age group). The most consumed food group across all age segments were non-alcoholic beverages followed by milk and dairy products and vegetables. Consumption of cereals and derivatives, milk and dairy products, sugars and sweets, and ready-to-eat meals by children was significantly higher than those by the adult and older adult populations (p ≤ 0.05). Conversely, intakes of vegetables, fruits, and fish and shellfish were significantly higher in adults and older adults (p ≤ 0.05). In order to comply with recommendations, adherence to the Mediterranean dietary patterns should be strengthened, especially amongst younger population groups. Therefore, substantial nutritional interventions may be targeted to improve the Spanish population’s dietary patterns nowadays. Full article

Excessive sodium consumption is associated with adverse health effects. An elevated dietary intake of salt (sodium chloride) has been related to high blood pressure or hypertension, a major but modifiable risk factor for cardiovascular disease, as well as to other ill health conditions. In the present work, our aim was to describe the contribution of foods to sodium consumption within the Spanish population in a representative sample from the “anthropometric data, macronutrients and micronutrients intake, practice of physical activity, socioeconomic data and lifestyles in Spain” (ANIBES) study (9–75 years), to identify high consumer groups, as well as the major food groups that contribute to sodium intake in the Spanish diet. Intakes were assessed by 3-day food records collected on a tablet device. Sodium intakes across the ANIBES study population exceeded recommendations, as total intakes reached 2025 ± 805 mg of sodium per day, that is approximately 5.06 g/day of salt (excluding discretionary salt, added at the table or during cooking). Sodium intakes were higher in males than in females and within the youngest groups. Main dietary sources of sodium were meat and meat products (27%), cereals and grains (26%), milk and dairy products (14%) and ready-to-eat meals (13%). Given the established health benefits of dietary salt reduction, it would be advisable to continue and even improve the current national initiatives of awareness and educational campaigns and particularly food reformulation to decrease overall salt intakes across the Spanish population. Full article

Diet is one of the key modifiable behaviors that can help to control and prevent non-communicable chronic diseases. Therefore, it is important to evaluate the overall diet composition of the population through non-invasive and independent indexes or scores as diet quality indexes (DQIs). The primary aim of the present work was to estimate the adequacy of the intake of critical nutrients in the Spanish “Anthropometry, Intake, and Energy Balance Study” (ANIBES) (n = 2285; 9–75 years), considering, as a reference, the European Food Scientific Authority (EFSA) values for nutrients for the European Union. We also assessed the quality of the diet for adults and older adults using four internationally accepted DQIs, namely the Healthy Diet Indicator (HDI), the Mediterranean Diet Score (MDS), the Mediterranean Diet Score-modified (MDS-mod), and the Mediterranean-Diet Quality Index (MED-DQI), as well as the ANIBES-DQI, stratified by education and income. The ANIBES-DQI was based on compliance with EFSA and Food and Agriculture Organization recommendations for a selected group of nutrients (i.e., total fat, saturated fatty acids (SFAs), simple sugars, fiber, calcium, vitamin C, and vitamin A), with a total range of 0–7. Misreporting was assessed according to the EFSA protocol, which allowed us to assess the DQIs for both the general population and plausible reporters. The majority of the Spanish population had high intakes of SFAs and sugars and low intakes of fiber, folate, and vitamins A and C. In addition, about half of the population had low DQI scores and exhibited low adherence to the Mediterranean diet pattern. Overall, older adults (>65–75 years) showed better DQIs than adults (18–64 years), without major differences between men and women. Moreover, primary education and low income were associated with low MDS and ANIBES-DQI scores. For the ANIBES-DQI, the percentage of the population with low scores was higher in the whole population (69.5%) compared with the plausible energy reporters (49.0%), whereas for medium and high scores the percentages were higher in plausible reporters (41.2% vs. 26.2% and 9.8% vs. 4.3%, respectively). In conclusion, the present study adds support to marked changes in the Mediterranean pattern in Spain, and low education and income levels seem to be associated with a low-quality diet. Additionally, the misreported evaluation in the ANIBES population suggests that this analysis should be routinely included in nutrition surveys to give more precise and accurate data related to nutrient intake and diet quality. Full article

The cell density-dependent mechanism, quorum sensing (QS), regulates the expression of virulence factors. Its inhibition has been proposed as a promising new strategy to prevent bacterial pathogenicity. In this study, 827 strains from the microbiota of sea anemones and holothurians were screened for their ability to produce quorum-sensing inhibitor (QSI) compounds. The strain M3-10, identified as Vibrio alginolyticus by 16S rRNA gene sequencing, as well as ANIb and dDDH analyses, was selected for its high QSI activity. Bioassay-guided fractionation of the cell pellet extract from a fermentation broth of strain M3-10, followed by LC–MS and NMR analyses, revealed tyramine and N-acetyltyramine as the active compounds. The QS inhibitory activity of these molecules, which was confirmed using pure commercially available standards, was found to significantly inhibit Chromobacterium violaceum ATCC 12472 violacein production and virulence factors, such as pyoverdine production, as well as swarming and twitching motilities, produced by Pseudomonas aeruginosa PAO1. This constitutes the first study to screen QSI-producing strains in the microbiota of anemones and holothurians and provides an insight into the use of naturally produced QSI as a possible strategy to combat bacterial infections. Full article