Search Results (21)

Lead and zinc pollution is a prevalent issue in agricultural soils surrounding lead and zinc mines, posing a serious risk to crop growth and soil health. Heavy metal-resistant, plant growth-promoting bacteria (PGPB) capable of supporting plant development under high metal exposure have significant potential for mitigating these deleterious effects. Here we isolated and identified the Pb- and Zn-resistant and plant growth-promoting bacterial strain Serratia ureilytica T6 based on 16S rRNA and average nucleotide identity (ANI) analysis. Furthermore, 14 strains (T1–T14) from a rice paddy soil irrigated by Pb-Zn mine effluent were isolated and identified, and their phytopromoting characteristics were determined. Genome analysis of S. ureilytica T6 showed a genome size of 5,102,941 bp, with G + C content of 59.74%. A total of 4822 genes were annotated by RAST, among which 15 genes were putatively associated with Pb-Zn resistance. The genome of S. ureilytica T6 was found to possess multiple genes associated with probiotic properties by a comparative analysis of KEGG, GO, and COG databases. Several taxonomic identifications of S. ureilytica T6 revealed that strain T6 is Gram-negative, facultative anaerobic and motile. The pH growth range of S. ureilytica T6 was between 4.00 and 9.50; temperature growth range was 4–37 °C; NaCl tolerance was 0–9%. S. ureilytica T6 displayed a high tolerance to a variety of heavy metals, with minimum inhibitory concentrations of 1.5 and 9 mmol·L⁻¹ for Pb and Zn. S. ureilytica T6 can utilize a variety of carbon sources and nitrogen sources. T6 has the ability to produce indole-3-acetic acid (IAA), siderophore, and phosphorus and potassium solubilization, and it was initially judged that strain T6 has the potential for plant growth-promoting ability. Different plant growth-promoting effects of T6 inoculations were observed in improving rice biomass, plant height, etc. We observed that with increasing Pb and Zn stress, SOD activity first increased and then decreased, while POD and CAT activities gradually decreased. The addition of S. ureilytica T6 significantly enhanced the activities of SOD, POD, and CAT in rice seedlings under low to moderate Pb and Zn stress but had no significant effect under high concentrations (150 mg·L⁻¹) of Pb or Zn. In addition, S. ureilytica T6 has the potential to be used as a phytoremediation tool. Full article

Background/Objectives: Despite extensive research on caffeine’s (CAF’s) ergogenic effects, evidence regarding its impact on anaerobic performance in female athletes remains limited and inconclusive. The aim of this study was to investigate the acute effects of 6 mg/kg⁻¹ caffeine on anaerobic performance, functional strength, agility, and ball speed in female soccer players. Methods: A randomized, double-blind, placebo-controlled crossover design was employed. Thirteen moderately trained female soccer players (age: 21.08 ± 1.11 years; height: 161.69 ± 6.30 cm; weight: 59.69 ± 10.52 kg; body mass index (BMI): 22.77 ± 3.50 kg/m²; training age: 7.77 ± 1.16 years; habitual caffeine intake: 319 ± 160 mg/day) completed two experimental trials (caffeine vs. placebo (PLA)), separated by at least 48 h. Testing sessions included performance assessments in vertical jump (VJ), running-based anaerobic sprint test (RAST), bilateral leg strength (LS), handgrip strength (HS), single hop for distance (SH), medial rotation (90°) hop for distance (MRH), change of direction (COD), and ball speed. Rating of perceived exertion (RPE) was also recorded. Results: CAF ingestion significantly improved minimum (p = 0.011; d = 0.35) and average power (p = 0.007; d = 0.29) during RAST. A significant increase was also observed in SHR (single leg hop for distance right) performance (p = 0.045; d = 0.44). No significant differences were found in VJ, COD, ball speed, LS, HS, SHL, MRHR, or MRHL (p > 0.05). RPE showed a moderate effect size (d = 0.65) favoring the CAF condition, though not statistically significant (p = 0.110). Conclusions: In conclusion, acute CAF intake at a dose of 6 mg/kg⁻¹ may enhance anaerobic capacity and lower-limb functional strength in female soccer players, with no significant effects on jump height, agility, or upper-body strength. Full article

Background: Early gut microbiome development is critical for neonatal health, and its dysbiosis may impact long-term animal productivity. This study examined the effects of parenteral Ceftiofur Crystalline Free Acid (CCFA) on the composition and diversity of the neonatal lamb fecal microbiome. The emergence of antimicrobial resistance genes associated with CCFA exposure was also investigated. Results: There were distinct microbial populations in the CCFA-treated lambs compared to the control group at each time point, with a highly significant decrease in alpha and beta diversity. The CCFA treatment showed a reduction in several key microbial taxa during nursing, but these differences were diminished by day 56. Unlike the control group, CCFA-treated lambs had core microbes potentially carrying multiple antibiotic resistance genes, including those for beta-lactam, fosfomycin, methicillin, and multidrug resistance. Methods: Twenty-four healthy neonatal lambs were randomly assigned to CCFA-treated (n = 12) and control (n = 12) groups. Fecal samples were collected on days 0, 7, 14, 28, and 56. Genomic DNA was extracted and sequenced using the Illumina MiSeq platform. Microbial composition was analyzed using the MG-RAST pipeline with the RefSeq database. Conclusions: Despite temporary reductions in critical bacterial populations during nursing, the early sheep fecal microbiome demonstrated resilience by repopulating after CCFA antibiotic disruption. While this highlights microbiota stability after short-course antibiotic exposure, the transient disturbance underscores potential risks to early gut health. Importantly, persistent CCFA resistance poses environmental dissemination risks, emphasizing the need for cautious antibiotic use in livestock to mitigate ecological impacts. Full article

Coastal waters are known for higher productivity and organic matter levels, which support a high diversity and abundance of microorganisms compared to some aquatic environments. The characterization of marine microbiomes can provide valuable information for evaluating the sustainability of coastal waters that are increasingly subjected to environmental and human impacts. Our study is the first metagenomic study realized on Moroccan Mediterranean coastal seawater. We analyzed and described the Gibraltar Detroit marine microbiome taxonomic and functional profiling using MG-RAST software. Shotgun sequencing revealed a predominance of bacterial taxa, particularly the Proteobacteria (57.29%) and Bacteroidetes (27.06%) phyla, alongside notable populations of eukaryotes, viruses, and archaea. Alphaproteobacteria and Gammaproteobacteria emerged as the dominant bacterial classes, while Flavobacteria represented a significant portion of Bacteroidetes. Functional profiling of the microbial community highlighted a wide array of metabolic pathways, emphasizing genes related to carbohydrate metabolism, amino acid synthesis, and protein processing. The marine microbiome exhibited essential biogeochemical activities, particularly in nitrogen, sulfur, and carbon cycles, with notable pathways including denitrification, thiosulfate oxidation, and carbon fixation. This functional diversity underlines the microbiome’s role in sustaining ecosystem health through nutrient cycling and organic matter degradation. Our findings offer a crucial baseline for understanding microbial community structure and resilience in Mediterranean coastal ecosystems, with implications for assessing future environmental and anthropogenic impacts on these microbial dynamics. Full article

Jeju, the largest island in Korea, is the most economically important in terms of marine aquaculture. We investigated the marine viral composition adjacent to Jeju Island over four seasons in 2022 and sequenced DNA libraries extracted from samples in March, June, September, and December using Illumina HiSeq 2000. We obtained 212,402, 186,542, 235,441, and 224,513 contigs from the four-season samples, respectively. Among the identified metagenomes, bacteriophages were dominant in all the samples. Bacillus phage G was the dominant species in March and June, whereas Pelagibacter phage HTVC 008M was the dominant species in September and December. Additionally, the number of viruses that infected algal hosts was higher in December than in other seasons. Marine viruses appeared in all seasons and infected marine vertebrates such as fish. Functional analysis using MG-RAST revealed that cell wall- and capsule-related metabolism groups were activated in March and June, whereas virulence-, disease-, and defense-related metabolism groups were activated in September and December. Conclusively, this study revealed seasonal changes in marine viral communities in the sea adjacent to Jeju Island. Our data will be useful in identifying emerging marine viral pathogens and for further community studies on marine organisms. Full article

This randomized, double-blinded, experimental study investigated the effects of a four-week daily pre-workout supplementation (200 mg caffeine, 3.3 g creatine monohydrate, 3.2 g β-alanine, 6 g citrulline malate, and 5 g BCAA) vs. placebo (isocaloric maltodextrin) on anaerobic (jumping, sprinting, agility, and the running-based anaerobic sprint test: RAST) and aerobic (Yo-Yo intermittent recovery test level 1) performance, as well as on body composition and selective muscle damage/health-related blood markers in well-trained basketball players during the in-season period. Eighteen basketball players (age: 24.4 ± 6.3 years, height: 185.7 ± 8.0 cm, weight: 85.7 ± 12.8 kg, body fat: 16.5 ± 4.2%) were randomly assigned into two groups: pre-workout supplement (PWS, n = 10) or placebo (PL, n = 8). PWS consumption increased aerobic performance (PWS: 8 ± 6%; PL: −2 ± 6%; p = 0.004) compared to PL. A significant decrease was observed in peak (F = 7.0; p = 0.017), average (F = 10.7; p = 0.005), and minimum power (F = 5.1; p = 0.039) following 4 weeks of supplementation in both groups. No other significant changes were observed between groups (p > 0.05). In conclusion, the consumption of the current PWS over a four-week period appears to positively influence the aerobic performance of well-trained basketball players during the in-season period. However, it does not appear to mitigate the observed decline in anaerobic power, nor does it affect performance in jumping, sprinting, and agility, or alter body composition or selective muscle damage/health-related blood markers. Full article

Shotgun metagenomic sequencing was used to investigate the diversity of the microbial community of Cheddar cheese ripened over 32 months. The changes in taxa abundance were compared from assembly-based, non-assembly-based, and mOTUs2 sequencing pipelines to delineate the community profile for each age group. Metagenomic assembled genomes (MAGs) passing the quality threshold were obtained for 11 species from 58 samples. Although Lactococcus cremoris and Lacticaseibacillus paracasei were dominant across the shotgun samples, other species were identified using MG-RAST. NMDS analysis of the beta diversity of the microbial community revealed the similarity of the cheeses in older age groups (7 months to 32 months). As expected, the abundance of Lactococcus cremoris consistently decreased over ripening, while the proportion of permeable cells increased. Over the ripening period, the relative abundance of viable Lacticaseibacillus paracasei progressively increased, but at a variable rate among trials. Reads attributed to Siphoviridae and Ascomycota remained below 1% relative abundance. The functional profiles of PMA-treated cheeses differed from those of non-PMA-treated cheeses. Starter rotation was reflected in the single nucleotide variant profiles of Lactococcus cremoris (SNVs of this species using mOTUs2), while the incoming milk was the leading factor in discriminating Lacticaseibacillus paracasei/casei SNV profiles. The relative abundance estimates from Kraken2, non-assembly-based (MG-RAST) and marker gene clusters (mOTUs2) were consistent across age groups for the two dominant taxa. Metagenomics enabled sequence variant analysis below the bacterial species level and functional profiling that may affect the metabolic interactions between subpopulations in cheese during ripening, which could help explain the overall flavour development of cheese. Future work will integrate microbial variants with volatile profiles to associate the development of compounds related to cheese flavour at each ripening stage. Full article

A pre-workout supplement’s (PWS; 200 mg caffeine, 3.3 g creatine monohydrate, 3.2 g β-alanine, 6 g citrulline malate and 5 g branched chained amino acid (BCAA) per dose) acute effects on the alactic (jumping, sprinting, agility), lactic (Running-Based Anaerobic Sprint Test, RAST) and aerobic performance (Yo-Yo Intermittent Recovery Test Level 1, Yo-Yo IRL1 VO_2max) of well-trained basketball players was investigated in this double-blind placebo-controlled study. Thirty players (age 18–31 years, height 166–195 cm, weight 70.2–116.7 kg, body fat 10.6–26.4%) were allocated to pre-workout (PWS, n = 15) or placebo (PL, n = 15) groups. Half of the participants in each group performed the evaluations without PWS or PL, while the rest consumed PWS or PL 30 min before the assessments (1st trial) and vice versa (2nd trial). Significant improvements in counter-movement jump (CMJ) (PWS: 4.3 ± 2.1%; PL: 1.2 ± 1.0%), agility (PWS: −2.9 ± 1.8%; PL: 1.8 ± 1.7%), RAST average (PWS: 18.3 ± 9.1%; PL: −2.2 ± 2.0%), minimum power (PWS: 13.7 ± 8.9%; PL: −7.5 ± 5.9%), and fatigue index (PWS: −25.0 ± 0.9%; PL: −4.6 ± 0.6%) were observed in the PWS group vs. the PL group (p < 0.05). No differences were found regarding sprinting, aerobic performance, and blood lactate concentrations. Thus, although players’ alactic and lactic anaerobic performance could be improved, peak power, sprinting and aerobic performance are not. Full article

Viruses are the most abundant living things and a source of genetic variation. Despite recent research, we know little about their biodiversity and geographic distribution. We used different bioinformatics tools, MG-RAST, genome detective web tools, and GenomeVx, to describe the first metagenomic examination of haloviruses in Wadi Al-Natrun. The discovered viromes had remarkably different taxonomic compositions. Most sequences were derived from double-stranded DNA viruses, especially from Myoviridae, Podoviridae, Siphoviridae, Herpesviridae, Bicaudaviridae, and Phycodnaviridae families; single-stranded DNA viruses, especially from the family Microviridae; and positive-strand RNA viruses, especially from the family Potyviridae. Additionally, our results showed that Myohalovirus chaoS9 has eight Contigs and is annotated to 18 proteins as follows: tail sheath protein, tco, nep, five uncharacterized proteins, HCO, major capsid protein, putative pro head protease protein, putative head assembly protein, CxxC motive protein, terl, HTH domain protein, and terS Exon 2. Additionally, Halorubrum phage CGphi46 has 19 proteins in the brine sample as follows: portal protein, 17 hypothetical proteins, major capsid protein, etc. This study reveals viral lineages, suggesting the Virus’s global dispersal more than other microorganisms. Our study clarifies how viral communities are connected and how the global environment changes. Full article

The aim of this study was to investigate and clarify the ambiguous taxonomy of Actinomyces naeslundii and its closely related species using state-of-the-art high-throughput sequencing techniques, and, furthermore, to determine whether sub-clusters identified within Actinomyces oris and Actinomyces naeslundii in a previous study by multi locus sequence typing (MLST) using concatenation of seven housekeeping genes should either be classified as subspecies or distinct species. The strains in this study were broadly classified under Actinomyces naeslundii group as A. naeslundii genospecies I and genospecies II. Based on MLST data analysis, these were further classified as A. oris and A. naeslundii. The whole genome sequencing of selected strains of A. oris (n = 17) and A. naeslundii (n = 19) was carried out using Illumina Genome Analyzer IIxe and Roche 454 allowing paired-end and single-reads sequencing, respectively. The sequences obtained were aligned using CLC Genomic workbench version 5.1 and annotated using RAST (Rapid Annotation using Subsystem Technology) release version 59 accessible online. Additionally, genomes of seven publicly available strains of Actinomyces (k20, MG1, c505, OT175, OT171, OT170, and A. johnsonii) were also included. Comparative genomic analysis (CGA) using Mauve, Progressive Mauve, gene-by-gene, Core, and Pan Genome, and finally Digital DNA-DNA homology (DDH) analysis was carried out. DDH values were obtained using in silico genome–genome comparison. Evolutionary analysis using ClonalFrame was also undertaken. The mutation and recombination events were compared using chi-square test among A. oris and A. naeslundii isolates (analysis methods are not included in the study). CGA results were consistent with previous traditional classification using MLST. It was found that strains of Actinomyces k20, MG1, c505, and OT175 clustered in A. oris group of isolates, while OT171, OT170, and A. johnsonii appeared as separate branches. Similar clustering to MLST was observed for other isolates. The mutation and recombination events were significantly higher in A. oris than A. naeslundii, highlighting the diversity of A. oris strains in the oral cavity. These findings suggest that A. oris forms six distinct groups, whereas A. naeslundii forms three. The correct designation of isolates will help in the identification of clinical Actinomyces isolates found in dental plaque. Easily accessible online genomic sequence data will also accelerate the investigation of the biochemical characterisation and pathogenesis of this important group of micro-organisms. Full article

Nitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate, a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere have not been fully explored. This study evaluates the diversity and abundance of nitrifying bacteria and archaea across different growth stages of maize using 16S amplicon sequencing. Moreover, the influence of environmental factors (soil physical and chemical properties) on the nitrifying communities was evaluated. Rhizosphere soil DNA was extracted using Nucleospin Soil DNA extraction kit and sequenced on Illumina Miseq platform. MG-RAST was used to analyze the raw sequences. The physical and chemical properties of the soil were measured using standard procedure. The results revealed 9 genera of nitrifying bacteria; Nitrospira, Nitrosospira, Nitrobacter, Nitrosovibrio, Nitrosomonas, Nitrosococcus, Nitrococcus, unclassified (derived from Nitrosomonadales), unclassified (derived from Nitrosomonadaceae) and 1 archaeon Candidatus Nitrososphaera. The Nitrospirae phyla group, which had the most nitrifying bacteria, was more abundant at the tasselling stage (67.94%). Alpha diversity showed no significant difference. However, the Beta diversity showed significant difference (p = 0.01, R = 0.58) across the growth stages. The growth stages had no significant effect on the diversity of nitrifying bacteria and archaea, but the tasselling stage had the most abundant nitrifying bacteria. A correlation was observed between some of the chemical properties and some nitrifying bacteria. The research outcome can be put into consideration while carrying out a biotechnological process that involves nitrifying bacteria and archaea. Full article

Spontaneously fermented dairy products have a long history, and present diverse microorganisms and unique flavors. To provide insight into the bacterial diversity, 80 different types of spontaneously fermented dairy product samples’ sequence data that were downloaded from MG-RAST and NCBI and 8 koumiss and 4 shubat were sequenced by the PacBio SMRT sequencing platform. All samples including butter, sour cream, cottage cheese, yogurt, koumiss, shubat, and cheese, were collected from various regions in Russia, Kazakhstan, Mongolia and Inner Mongolia (China). The results revealed that Firmicutes and Proteobacteria were the most dominant phyla (>99%), and 11 species were identified with a relative abundance exceeding 1%. Furthermore, Streptococcus salivarius, Lactobacillus helveticus, Lactobacillus delbrueckii, Enterobacter xiangfangensis, and Acinetobacter baumannii were the primary bacterial species in the fermented dairy product samples. Principal coordinates analysis showed that koumiss and shubat stood out from the other samples. Moreover, permutational ANOVA tests revealed that the types of fermented dairy products and geographical origin significantly affected microbial diversity. However, different processing techniques did not affect microbial diversity. In addition, results of hierarchical clustering and canonical analysis of the principal coordinates were consistent. In conclusion, geographical origin and types of fermented dairy products determined the bacterial diversity in spontaneously fermented dairy product samples. Full article

This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment. Full article

An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample. Full article

Aim: The aim of the study was to evaluate the effects of 16 weeks of a low dose of magnesium creatine chelate supplementation on repeated sprint ability test (RAST) results in elite soccer players. Materials: Twenty well-trained soccer players participated in the study. The players were divided randomly into two groups: the supplemented group (SG = 10) and placebo group (PG = 10). Out of the 20 subjects selected for the study, 16 (SG = 8, PG = 8) completed the entire experiment. The SG ingested a single dose of 5500 mg of magnesium creatine chelate (MgCr-C), in 4 capsules per day, which was 0.07 g/kg/d. The PG received an identical 4 capsules containing corn starch. Before and after the study, the RAST was performed. In the RAST, total time (TT), first and sixth 35 m sprint length (s), average power (AP) and max power (MP) were measured. Additionally, before and after the test, lactate LA (mmol/L) and acid–base equilibrium pH (-log(H⁺)), bicarbonates HCO₃⁻ (mmol/L) were evaluated. Also, in serum at rest, creatinine (mg/dL) concentration was measured. Results: After the study, significantly better results in TT, AP and MP were observed in the SG. No significant changes in the RAST results were observed in the PG. After the study, significant changes in the first 35 m sprint, as well as the sixth 35 m sprint results were registered in the SG, while insignificant changes occurred in the PG. A significantly higher creatinine concentration was observed. Also, a higher post-RAST concentration of LA, HCO₃⁻ and lower values of pH were observed in April, May and June compared with baseline values. Conclusions: The long timeframe, i.e., 16 weeks, of the low dose of magnesium creatine chelate supplementation improved the RAST results in the SG. Despite the long period of MgCr-C supplementation, in the end of the study, the creatinine level in the SG reached higher but still reference values. Full article