Archives of Microbiology

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LC-MS of a crude compound 1 in positive (above) and negative mode
UV absorbance (above) and mass spectrum for crude compound 1 in positive mode
13 C-NMR (above) and HSQC spectrum of crude compound 1
Mass spectrum of grevilline B, apigenin and aflatoxin G2
  • Kamel H. ShakerKamel H. Shaker
  • Moustafa M. ZohairMoustafa M. Zohair
  • Amal Z. HassanAmal Z. Hassan
  • [...]
  • Warda E. AshourWarda E. Ashour
The antimicrobial activity of endophytic fungi isolated from Euphorbia milii was evaluated against Gram-positive, Gram-negative bacteria, unicellular yeast, and filamentous fungi. Chaetomium ovatoascomatis NRC was identified morphologically and genetically as the most active strain. The total ethyl acetate extract of C. ovatoascomatis NRC demonstrated significant antimicrobial activity against Gram-negative; Escherichia coli , Salmonella enteric , and fungi; Aspergillus niger with MIC of 62.5 ug/ml. Whereas n -hexane fraction demonstrated broader activity against Gram-positive; Bacillus subtilis , Lactobacillus cereus , Gram-negative; Escherichia coli and Salmonella enteric , fungi; Candida albicans and F. solani . LC–MS/MS analysis of ethyl acetate strain extract and GC–MS analysis of the n -hexane fraction were used to identify the metabolites of the strain extract. LC–MS/MS determined three major metabolites with potential antimicrobial activities including grevilline B, aflatoxin G2 and apigenin. GC–MS analysis of n -hexane fraction tentatively identified 30 compounds, where 9,12-octadecadienoic acid methyl ester was the major compound.
 
Scanning electron micrograph of strain TRM 95111T cultivated on YMA medium for 3 days at 25 °C. Bar, 2 μm (left). Scanning electron micrograph of strain TRM 95001T cultivated on NA medium for 4 days at 25 °C. Bar, 2 μm (right)
Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationships of strain TRM95111T, TRM95001T and their closely related Rhizobium and Shinella species. The corresponding algorithms were achieved using the MEGA X. The topology of the phylogenetic tree was evaluated by the bootstrap resampling method of Felsenstein (1985) with 1000 replicates. Only values above 50% were indicated. Azorhizobium caulinodans ORS571T was used as an outgroup. Bar, 0.01 substitutions per nucleotide position
Phylogenetic tree based on core-proteome average amino acid identity (cpAAI) sequences showing the relationships of strain TRM95111T, TRM95001T and their closely related Rhizobium and Shinella species. The numbers above branches are cpAAI pseudobootstrap support values > 54% from 100 replications, with an average branch support of 97.1%. Azorhizobium caulinodans ORS571T was used as an outgroup
  • Hongling ShenHongling Shen
  • Xiaoxia LuoXiaoxia Luo
  • Zhanfeng XiaZhanfeng Xia
  • Chuanxing WanChuanxing Wan
Two strains (TRM95111T and TRM95001T) of Gram-stain-negative, aerobic, rod-shaped microbes were isolated from the nodule and rhizosphere of Lotus japonicus grown in the campus of Tarim University in Alar, Xinjiang, China. Strain TRM95111T and strain TRM95001T shared 93.1% 16S rRNA gene sequences similarity with each other and had 98.2 and 97.9% 16S rRNA gene sequence similarity to the closest species Rhizobium subbaraois JC85T and R. halotolerans AB21T by EzBioCloud blast, respectively. Phylogenetic analyses based on 16S rRNA gene sequences, housekeeping gene sequences and core-proteome average amino acid identity (cpAAI) showed that two strains belonged to the genus Rhizobium. The value of digital DNA–DNA hybridization (dDDH) between strain TRM95111T and the closest strain R. subbaraonis JC85T was 21.8%, respectively. The dDDH value between strain TRM95001T and the closest strains R. tarimense PL-41T was 27.1%. Whole-genome average nucleotide identity (ANI) values of the strain TRM95111T were 75.6–79.3% and strain TRM95001T were 79.2–83.8%, compared to their closely related strains. The G + C content values of strain TRM95111T and TRM95001T were 65.1 and 60.7 mol%, respectively. Two isolates contained predominant quinone of Q-10 and the major fatty acids was C18:1ω7c and they were sensitive to 1 μg of amikacin and kanamycin. The polar lipids of strain TRM95111T included unidentified aminophospho lipids (APL1-3), unidentified phospholipids (PL1-2), phosphatidylcholine (PC), unidentified lipids (L1-5) and phospholipids of unknown structure containing glucosamine (NPG), compared to the polar lipids of strain TRM95001T including unidentified aminophospho lipids (APL1-3), unidentified phospholipids (PL1-2), phosphatidylcholine (PC), unidentified lipids (L2-5), hydroxy phosphatidyl ethanolamine (OH-PE) and phospholipids of unknown structure containing glucosamine (NPG). Nodulation tests showed that two strains could induce nodules formation in L. japonicus. Based on the genomic, phenotypic and phylogenetic analyses, strain TRM95111T and strain TRM95001T are suggested to represent two new species of the genus Rhizobium, whose names are proposed as Rhizobium alarense sp. nov. and Rhizobium halophilum sp. nov. The type strains are TRM95111T (=CCTCC AB 2021116T =JCM34826T) and TRM950011T (=CCTCC AB 2021095T =JCM34967T), respectively.
 
Phylogenetic trees of arsB and arsC (a), arsA and arsR (b), aioA and aioB (c), acr1 and acr3 (d), and arrA and arsD (e) proteins in different bacterial species. The trees were constructed following maximum parsimony method
Three D protein structure of marker genes in different bacterial species: i–iv represent arsB, arsC, arsR, and acr1 in Pseudomonas aeruginosa PAO1, respectively. v–ix represent arsB, arsC, arsD, arsR, and acr1 in Escherichia coli ATCC 11,775, respectively. x–xiv represent arsB, arsC, arsD, arsR, and acr1 in Klebsiella pneumoniae ATCC 13,883 respectively. xv–xviii represent acr3, arsA, arsB, arsD in Ochrobactrum tritici CCUG 47,104 respectively. xix and xx represent arrA, arsC in Shewanella sp. ANA-3, respectively. xxi-xxiii represent aioB, arsB, and arsR in Staphylococcus aureus ATCC 1260, respectively. xxiv–xxvi represent acr1, acr3 and ars3 in Acinetobacter baumannii ATCC 19,606, respectively. xxvii and xxviii represent Acr1 and arsD in Citrobacter freundii ATCC 8090, respectively. xxix–xxxi represent arsA, arsD, and arsR in Klebsiella oxytoca: ATCC 13,182, respectively
Isolated indigenous bacteria grown on nutrient agar medium supplemented different concentration of As(III) and As(V). Layout (below figures) represents the distribution of different bacterial isolates under different concentration of As(III) and As(V). Sources of individual isolates are given in Supplementary Table 1
  • Md. Numan IslamMd. Numan Islam
  • Md SuzauddulaMd Suzauddula
  • Zubayed AhamedZubayed Ahamed
  • [...]
  • Md. Mahmudul HasanMd. Mahmudul Hasan
Marker proteins play a significant role in bacterial arsenic (As) transformation. Phylogenetic analysis and three-dimensional (3D) characteristics of As transforming bacterial marker proteins guide the evolutionary origin and As transforming potential of the species. Indeed, As-tolerant bacteria also show a significant level of As transformation. Hence, characterization of As transforming bacterial marker proteins, isolation of As transforming bacteria, and proper integration of the findings may guide to elucidate how bacteria transform As. Therefore, phylogenetic analysis and 3D characterization of As transforming bacterial marker protein following isolation of potential indigenous As-tolerant indigenous bacteria were done to explore the mechanism of bacterial As transformation. Phylogenetic analysis of ten As transforming marker proteins (arsA, arsB, arsC, arsD, arsR, aioA, arrA, aioB, acr1, and acr3) in 20 potential bacterial genomes (except 19 for the acr3) were studied. Some bacterial genomes featured up to five marker proteins, and therefore, 3D characteristics of the marker proteins were analyzed in those genomes having three-to-five marker proteins. In phylogeny, species in close clades represent their phylogenetic resemblances and may have similar functions. P. aeruginosa, E. coli, and K. pneumonia were found to be more effective due to having the highest number (five) of marker proteins. In 3D protein modeling, most of the marker proteins were found to be active. Among 19 indigenous bacterial isolates, multiple isolates showed tolerance up to 50 mM As(III) and 250 mM As(V), which may potentially transform a significant quantities of As. Hence, integration of the results of phylogenetic analysis, 3D protein characteristics, and As tolerance in the bacterial isolates could guide to explore the mechanism of how bacteria transform As at cellular and molecular levels.
 
  • Jusna NandeibamJusna Nandeibam
  • Y Randhir Babu SinghY Randhir Babu Singh
  • K Chandradev SharmaK Chandradev Sharma
  • [...]
  • S Indira DeviS Indira Devi
134 bacterial strains were isolated from phumdis of Loktak Lake. Through 16S rRNA sequencing, Bacillus sp. (23, 17.1%), Staphylococcus sp. (14, 10.4%), Pseudomonas sp. (11, 8.2%) and Acinetobacter sp. (8, 5.9%) were identified as the predominant bacterial taxa of Loktak Lake. B. pumulis (12, 8.9%), S. arlettae (4, 2.9%), P. knackmussii (6, 4.4%) are the leading species of Bacillus, Staphylococcus and Pseudomonas, respectively. Similarly, A. seifertii (2, 1.4%) and A. calcoaceticus (2, 1.4%) are the common species of Acinetobacter. 75 (55.9%) bacterial strains showed the ability to hydrolyze one or more extracellular enzymes tested. Among the extracellular enzymes produced by the bacterial isolates, the presence of elastase activity cannot be underestimated, since the enzyme is involved in the process of bacterial lung infection. Phosphate solubilizing activity could be seen in 11.1% of the bacterial isolates. 27 (20.1%) of the strains shown to have antagonistic activity against one or more tested pathogens. An isolate, MRC 52 showed antagonistic activity against eleven different pathogens including carbapenem resistant E. coli which was further subjected to extraction and identification of the biomolecule exerting the antimicrobial property. Based on GC–MS analysis, the bioactive compound was identified as phenyl ethyl alcohol.
 
In this study, the acute toxicity effects of a fluorescent xanthene dye, Rhodamine B (RhB), widely used in textile, paper, and leather industries was investigated on a freshwater microalgae Chlorella vulgaris. The acute toxicity of RhB on C. vulgaris was determined by examining the growth, cell morphology, pigment production, protein content, and the activities of oxidative stress enzymes. Based on the results of the toxicity study of 24–96 h, the median inhibitory concentration (IC50) values ranged from 69.94 to 31.29 mg L⁻¹. The growth of C. vulgaris was conspicuously inhibited by RhB exposure, and the cell surfaces appeared to be seriously shrunk in SEM analysis. The growth of C. vulgaris was hindered after exposure to graded concentrations (10–50 mg L⁻¹) of RhB. A significant reduction in growth rate, pigment synthesis (chlorophyll a, chlorophyll b, and carotenoid), and protein content was recorded in a dose-dependent manner. After 96 h exposure of C. vulgaris to 50 mg L⁻¹ RhB, chlorophyll a, chlorophyll b, carotenoids, and protein contents were reduced by 71.59, 74.90, 65.84, and 74.20%, respectively. The activities of the antioxidant enzymes peroxidase (POD), and catalase (CAT) also increased markedly in the presence of RhB. A notable effect was observed on oxidative enzymes catalase and peroxidase, indicating that oxidative stress may be the primary factor in the inhibition of growth and pigment synthesis. Consequently, the experimental acute toxicity data were compared to the QSAR prediction made by the ECOSAR programme. Results showed that the experimental acute toxicity values were 67.74-fold lower than the ECOSAR predicted values. The study provides convincing evidence for the metabolic disruption in the ubiquitous microalgae C. vulgaris due to the RhB dye toxicity. Graphical abstract
 
This study aims to reveal initial bacterial consortia of Ezine PDO cheeses comprehensively by following a metagenomic approach. A total of 8 artisanal Ezine cheese samples were collected from the Bayramiç and Ezine districts of Çanakkale province of Turkey. Ezine cheese was found to contain Firmicutes, Bacteroidetes, and Proteobacteria phyla dominantly. Streptococcus, Lactococcus, and Lactobacillus genera dominated the microbiota with relative abundances of 4.47–56.07%, 7.33–20.34%, and 1.21–25.12%, respectively, followed by Bacteroides and Prevotella genera. Excluding two cheese samples obtained from the Ezine district, the most dominant species was Streptococcus thermophilus (8.24–54.34%). It was also found in greater proportions in the cheeses of the Bayramiç district. Unexpectedly, Lactobacillus graminis (11.50–23.63%) was the most abundant species in two samples collected from the Ezine district. However, lower bacterial diversity was determined in the samples collected from the Bayramiç district. The lowest species richness was 129 OTU-species in the cheeses from the Bayramiç district while the highest species richness was 267 OTU-species in cheeses from the Ezine district. In addition, the Simpson index was the highest in cheeses from the Ezine district, where different species were evenly distributed. Permutational multivariate analysis of variance tests also confirmed that the differences in the structure of bacterial consortia in cheeses from two different districts were statistically significant. This study will provide pioneer data for further investigations on the role of complex bacterial composition in maintaining and improving the quality and safety of Ezine cheese.
 
Diverse thermophilic microorganisms with the potential to withstand extreme physiological conditions have long been investigated and explored for human commercial benefit. Thermozymes with distinct functional and structural properties isolated from these thermophiles are known to have high thermostability without significant loss of specific enzyme activity. Thermophiles isolated and characterised from the thermophilic ecological niche of India are well documented. There is a plethora of work in the literature emphasising its industrial significance. However, in-depth knowledge of the thermophilic oxidoreductase group of enzymes (Oxizymes) is restricted. Sulfur Oxygenase Reductases or Sulfur Oxygen-Reductases (SORs) are a group of thermophilic oxizymes reported predominantly from thermophilic and mesophilic archaea and bacteria, which catalyse oxygen-dependent disproportionation reactions of elemental sulfur, producing sulfite, thiosulfate, and sulphide. There have been few reports on isolated and characterised SORs from the Indian geothermal niche. The review article will highlight the SORs reported till date with a concise overview of different archaeal and bacterial species producing the enzymes. Based on the literature available till date, characteristics including physico-chemical properties, amino acid sequence homology, conserved motifs and their 3D structure comparison have been discussed. In-silico sequence and structure level preliminary comparative analysis of various SORs has also been discussed. However, a few SORs whose structural information is not reported in the protein data bank have been modelled to enrich our analysis.
 
This study encompasses isolation and screening of heavy metal-resistant fungal and bacterial strains from tannery solid waste (TSW). Twelve fungal strains and 25 bacterial strains were isolated from TSW. The growth of fungal strains was observed against different heavy metals ranging from 10 to 1050 mg L⁻¹ and the growth of bacteria was observed in metal concentrations ranging from 10 to 1200 mg L⁻¹. Five multi-metal-resistant fungal isolates belonging to the genus Trichoderma and ten bacterial isolates belonging to the genus Bacillus showed good metal resistance and biosorption potential. They were identified through molecular techniques, fungi based on ITS region ribotyping, and bacteria based on 16S rRNA ribotyping. The fungal strains were characterized as T. hamatum (TSWF-06), T. harzianum (TSWF-11), T. lixii (TSWF-02), and T. pseudokoningii (TSWF-03, TSWF-10). The bacterial strains were characterized as Bacillus xiamenensis (TSW-02), B. velezensis (TSW-05), B. piscis (TSW-06), B. safensis (TSW-10), B. subtilis (TSW-14, TSW-15, TSW-17) B. licheniformis (TSW-19), B. cereus (TSW-20), and B. thuringiensis (TSW-22). The fungal strains, namely, T. pseudokoningii (TSWF-03) and T. harzianum, proved to be two multi-metal-resistant strains with good biosorption efficiency. Unlike fungi, bacterial strains showed metal-specific resistance. The strains Bacillus xiamenensis, B. subtilis (TSW-14), and B. subtilis (TSW-15) showed good biosorption efficiency against Cr, B. safensis against Cu, B. piscis, and B. subtilis (TSW-17) against Pb and B. licheniformis and B. thuringiensis against Zn. The autochthonous fungal and bacterial strains can therefore be employed to clean metal-contaminated environments.
 
Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of IMAU99125T, IMAU99674 and the type strains of related species. The stability of the tree was assessed using bootstrap analysis of 1000 replicates with MEGA 6. Bar = 0.01 changes per nucleotide position
Whole-genome phylogenetic tree with rectangular cladogram layout containing isolates IMAU99125T, IMAU99674 and closely related members of the genus Streptococcus
Heat map of ANI values based on the whole genome of isolate IMAU99125T and closely related members of the genus Streptococcus
Two bacterial strains were isolated from the breast milk of two healthy nursing mothers. The isolates were Gram-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of the 16S rRNA gene sequences of strain IMAU99125T shared 99.7 and 99.6% similarity with Streptococcus mitis ATCC 49456 T and Streptococcus pseudopneumoniae ATCC BAA-960 T, respectively. The nearly complete 16S rRNA gene sequences of IMAU99125T and IMAU99674 strains were very closely related (with only 0.06% difference between them). Sequence analysis of the gyrB and rpoB genes also indicated that IMAU99125T was closely related to S. mitis ATCC 49456 T (94.7% and 97.1%, respectively) and S. pseudopneumoniae ATCC BAA-960 T (94.4% and 97.1%, respectively). Average nucleotide identity (ANI) values between strain IMAU99125T and S. mitis ATCC 49456 T and S. pseudopneumoniae ATCC BAA-960 T, were 93.3% and 92.7%, respectively. Genome-to-genome distance (GGD) values between strain IMAU99125T and S. mitis ATCC 99125 T and S. pseudopneumoniae ATCC BAA-960 T were 53.4% (50.7–56.0) and 50.4% (47.7–53.0), respectively. The major fatty acids of the strain were C16:0 (51.4%). On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two strains be classified as representing a novel species of the genus Streptococcus, namely Streptococcus humanilactis sp.nov. The type strain is IMAU99125T (= GDMCC 1.1876 T = KCTC 21157 T). The genome of Streptococcus humanilactis sp. nov. is comprised of 2,027,143 bp. The DNA G + C content of the strain is 40.0 mol%.
 
Acetyl-coenzyme A (CoA) synthetase (Acs) links cellular metabolism and physiology by catalyzing acetate and CoA into acetyl-CoA. However, the biological roles of Acs are not well studied in entomopathogenic fungi. In this study, two Acs proteins (BbAcs1 and BbAcs2) was functionally characterized in the filamentous insect pathogenic fungus Beauveria bassiana. BbAcs1 and BbAcs2 localize in cytoplasm and peroxisome, respectively. BbAcs1 contributes to vegetative growth on fatty acids as carbon source, and BbAcs2 did not. Both genes did not contribute to fungal response to stresses. The BbAcs1 loss conferred a slight influence on conidiation, and did not result in the defects in blastospore formation. On the contrary, BbAcs2 significantly contributes to lipid metabolism in germlings, blastospore formation, and virulence. The results indicated that Acs2 played a more predominant role than Acs1 in B. bassiana, which links the acetyl-CoA metabolism with the lifestyle of entomopathogenic fungi.
 
Mosquitoes are a vector for many dreadful diseases known for their public health concern. The continued use of synthetic insecticides against vector control has led to serious environmental impacts, human health problems, and the development of insect resistance. Hence, alternative mosquito control methods are needed to protect the environment and human health. In the present study, the bioefficacy of (2-(((2-ethyl-2 methylhexyl)oxy)carbonyl) benzoic acid isolated from Bacillus pumilus were tested against Aedes aegypti, Culex quinquefasciatus and Anopheles stephensi. The isolated bioactive compound was characterized through thin layer chromatography (TLC), UV–visible spectroscopy (UV), Fourier-transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, and gas chromatography–mass spectrometry analysis. The pure compound caused a high percent mortality rate in a dose-dependent manner, the obtained values were 96, 82, 69, 50 and 34%; 86, 72, 56, 43, and 44%; 100, 90, 83, 70 and 56% against Ae. aegypti, Cx. quinquefasciatus, and An. stephensi respectively. The effective lethal concentration values (LC50) were 13.65, 14.90 and 9.64 ppm against Ae. aegypti, Cx. quinquefasciatus, An. Stephensi, respectively. The effect of (2-(((2-ethyl-2 methylhexyl)oxy)carbonyl) benzoic acid significantly increased the superoxide dismutase, catalase, α, β esterase and Glutathione-S-transferase level after 24 h of the treatment period. The comet assay confirmed that isolated compound causes DNA damage in all tested insects. Histopathological examinations of treated larvae showed shrunken body posture, damaged epithelial cells and microvillus as compared to control organisms. The biosafety of the isolated compound was assessed against G. affinis and did not produce mortality which confirmed that the activity of the isolated compound is species specific. The current study concludes that the critical success factors of new insecticidal agent development are based on the eco-compatibility and alternative tools for the pesticide producing industry.
 
Mosquitoes are a vector for many dreadful diseases known for their public health concern. The continued use of synthetic insecticides against vector control has led to serious environmental impacts, human health problems, and the development of insect resistance. Hence, alternative mosquito control methods are needed to protect the environment and human health. In the present study, the bioefficacy of (2-(((2-ethyl-2 methylhexyl)oxy)carbonyl) benzoic acid isolated from Bacillus pumilus were tested against Aedes aegypti, Culex quinquefasciatus and Anopheles stephensi. The isolated bioactive compound was characterized through thin layer chromatography (TLC), UV–visible spectroscopy (UV), Fourier-transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, and gas chromatography–mass spectrometry analysis. The pure compound caused a high percent mortality rate in a dose-dependent manner, the obtained values were 96, 82, 69, 50 and 34%; 86, 72, 56, 43, and 44%; 100, 90, 83, 70 and 56% against Ae. aegypti, Cx. quinquefasciatus, and An. stephensi respectively. The effective lethal concentration values (LC50) were 13.65, 14.90 and 9.64 ppm against Ae. aegypti, Cx. quinquefasciatus, An. Stephensi, respectively. The effect of (2-(((2-ethyl-2 methylhexyl)oxy)carbonyl) benzoic acid significantly increased the superoxide dismutase, catalase, α, β esterase and Glutathione-S-transferase level after 24 h of the treatment period. The comet assay confirmed that isolated compound causes DNA damage in all tested insects. Histopathological examinations of treated larvae showed shrunken body posture, damaged epithelial cells and microvillus as compared to control organisms. The biosafety of the isolated compound was assessed against G. affinis and did not produce mortality which confirmed that the activity of the isolated compound is species specific. The current study concludes that the critical success factors of new insecticidal agent development are based on the eco-compatibility and alternative tools for the pesticide producing industry.
 
a Principal component analysis (PCA) based on the relationship between the examined variables including soil parameters (pH, clay, silt and sand, WHC: water holding capacity and OM: organic matter), aerobic cultivable bacterial number, benzene and the sum of PAHs content, b Heatmap indicating Spearman correlation coefficient between variables
Abundance and distribution of bacteria and aromatics hydrocarbons in each soil sample
Maximum Likelihood trees showing the phylogenetic relationships between partial 16S rRNA sequences of our isolates and those of closely relates species and some hydrocarbonoclastic genera a tree for Gram-negative bacteria with Flavobacterium naphthae strain Brt-M (NR 159,280.1) as an outgroup, b tree for Gram-positive bacteria and Desulfonispora thiosulfatigenes strain GKNTAUT (NR 026497.1) which served as an outgroup. Sequences were retrieved from NCBI database. Numbers on branches represent bootstrap values with 1000 repetitions (> 50%). The scale bar indicates 6% of sequence divergence for the first tree and 4% for the second one
Algerian petrochemical industrial areas are usually running spills and leakages of hydrocarbons, which constitutes a major source of toxic compounds in soil such as aromatic hydrocarbons. In this paper, samples of crude oil-polluted soil were collected from Skikda’s oil refinery and were subjected to mono and polyaromatic hydrocarbons threshold assessment. Soil physicochemical parameters were determined for each sample to examine their response to pollution. Amid 34 isolated bacteria, eleven strains were selected as best Biosurfactants (Bs)/Bioemulsifiers (Be) producers and were assigned to Firmicutes and Proteobacteria phyla based on molecular identification. Phylogenetic analysis of partial 16S rDNA gene sequences allowed the construction of evolutionary trees by means of the maximum likelihood method. Accordingly, strains were similar to Bacillus spp., Priesta spp., Pseudomonas spp., Enterobacter spp. and Kosakonia spp. with more than 95% similarity. These strains could be qualified candidates for an efficient bioremediation process of severally polluted soils.
 
Maximum-likelihood tree based on 16S rRNA gene sequences of strains PPLLT and reference strains of the family Desulfocapsaceae. A total of 1477 positions were used in the final dataset. Desulfobulbus propionicus DSM 2032 T was used as an outgroup. The phylogenetic tree was inferred using the maximum likelihood method and Kimura 2-parameter model + Gamma distributed with Invariant sites. Bootstrap values (percentages of 1000 replications) only 50% or more are shown at nodes
A novel sulfate-reducing bacterium, strain PPLLT, was isolated from marsh soil. Cells of strain PPLLT were rod-shaped with length of 1.5 μm and width of 0.7 μm. Growth was observed at 22–37 °C (optimum 35 °C) and pH 6.8–8.4 (optimum 7.3). Lactate, succinate, fumarate, formate and malate were utilized as electron donors for sulfate reduction. Fermentative growth was not observed on tested organic acids. Besides sulfate, sulfite, thiosulfate and elemental sulfur were utilized as electron acceptors. Hydrogen is used only in the presence acetate or yeast extract. The major fatty acid was C16:0. The complete genome of strain PPLLT was composed of a circular chromosome with length of 4.2 Mbp and G + C content of 57.7 mol%. Sequence analysis of the 16S rRNA gene showed that strain PPLLT was affiliated with the genus Desulfofustis in the family Desulfocapsaceae. On the basis of differences in the phylogenetic and phenotypic properties between the strain and the type strain of the genus Desulfofustis, strain PPLLT (DSM 110475T = JCM 39161T) is proposed as the type strain of a new species, with name of Desulfofustis limnaeus sp. nov.
 
Antibacterial activities of the bacterial extract and formulation against AE. coli, BS. pyogenes, CS. aureus, and DP. aeruginosa
Photomicrographs representing the in-vitro wound healing potential of B. amyloliquefaciens MTCC 12716 extract: L929 cells were incubated in the presence or absence of the bacterial extract and the formulation. The images were captured at 24 and 48 h. A Extent of closure obtained under control conditions after 24 h and B 48 h. C–D Migration of cell line towards the scratch made on fibroblast cell line treated with the bacterial extract at its MIC and E–F that observed after the addition of 25 μg mL⁻¹ of extract-loaded formulation. The experiment was performed independently at least three times. G Graphical representation of scratch wound healing assay measured using Image J-MRI Image analysis software. The Y-axis represents the wound area in arbitrary units, whereas X-axis-treated groups at 0 and 48 h. Control—untreated fibroblast cell line, extract—treated with ethyl acetate extract of the bacterium, and formulation—topical formulation prepared with bacterial extract/oleoresin as the key ingredient. Data were represented as mean ± SD, where n = 3
Various studies conducted to evaluate the stability of the formulation. A Total viable count. B MacConkey Agar plate with no growth of Gram-negative pathogens. C Absence of E. coli on eosin methylene blue agar plate. D Zone of inhibition observed with the formulation O3 and a synthetic antibacterial cream C as standard
The inevitability to develop novel antimicrobial agents has considerably increased because of mounting alarms concerning multidrug-resistant microbial strains. The present study evaluated an antibacterial and wound healing topical formulation prepared with the ethyl acetate extract of marine symbiotic Bacillus amyloliquefaciens MTCC 12716 as the basic ingredient and the grafted macroalgal polysaccharide as the gel base with an appropriate proportion of natural stabilizing agents. The formulation exhibited potent antibacterial activities against clinical isolates of Staphylococcus aureus (18 mm inhibition zone) and Pseudomonas aeruginosa (19 mm) causing infection when compared with commercially available antimicrobial cream clindamycin. The in-vitro results indicated that the organic extract of B. amyloliquefaciens MTCC 12716 at its MIC and the formulation sealed the wound by 78 and 94%, respectively, at 48 h in the scratch-induced L929 cells, compared to 84% exhibited by clindamycin. The topical formulation of marine symbiotic Bacillus induced greater than 80% viability of the normal fibroblasts compared to 78% exhibited by clindamycin, when administered at a dose of 25 μg mL⁻¹. The studied antibacterial formulation could accelerate the wound healing by prompting the migration of fibroblasts towards the artificially created wound resulting in rapid wound closure, and at an even higher concentration of formulation, it displayed no cytotoxicity on L929 cells. The stability studies showed that the formulation maintained its physicochemical characteristics and minimal growth (<10 cfu g⁻¹) of bacteria on the plates throughout the time period of 18 months at 30 °C and 65% relative humidity. This study has established the antibacterial and wound healing potential of a topical formulation of marine symbiotic B. amyloliquefaciens. Graphical Abstract
 
Aim of this study was to optimize the production of Ligninolytic enzyme for the degradation of complex pollutants present in pulp paper industrial effluent (PPIE). Two ligninolytic enzyme-producing bacterial strains were isolated from PPIE and identified as Bacillus paramycoides strain BL2 (MZ676667) and Micrococcus luteus strains BL3 (MZ676668). The identified bacterial strain Bacillus paramycoides strain BL2 showed optimum production of LiP (4.30 U/ml), MnP (3.38 U/ml) at 72 h of incubation, while laccase (4.43 U/ml) at 96 h of incubation. While, Micrococcus luteus strains BL3 produced maximum LiP (3.98) and MnP (3.85 U/ml) at 96 h of incubation and maximum laccase (3.85 U/ml) at 72 h of incubation, pH 7-8, and temperatures of 30–35 °C. Furthermore, in the presence of glucose (1.0%) and peptone (0.5%) as nutrient sources, the enzyme activity of consortium leads to reduction of lignin (70%), colour (63%) along with COD (71%) and BOD (58%). The pollutants detected in control i.e. 3.6-Dioxa-2,7-disilaoctane, 2-Heptnoic acid,trimethylsilyl ester, 7-Methyldinaphtho [2,1-b,1’,2’-d] silole, Hexadeconoic acid, trimethylysilyl ester, Methyl1(Z)-3,3-dipheny.1-4-hexenoale, 2,6,10,14,18,22-Tetracosahexane,2,2-dimethylpropyl(2Z,6E)-10,11epoxy5,6 Dihyrostigmasterol, acetate were completely diminished. The toxicity of PPIE was reduced up to 75%. Hence, knowledge of this study will be very useful for industrial sector for treatment of complex wastewater.
 
Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences of strain 2V75T and other closely related species. Filled circles indicate branches that were recovered with all three methods (neighbor-joining, maximum-likelihood and minimum-evolution). Percentages bootstrap values above 70% (1000 replicates) are shown at branch nodes (NJ/ML/ME). Coenonia anatina LMG 14382 T (Y17612) was used as the out-group. Bar, 0.01 substitutions per nucleotide position
Phylogenetic tree based on alignment of 120 conserved proteins from 16 genomes of related strains showing the taxonomic position of strain 2V75T. Percentages bootstrap values above 50% (1000 replicates) are shown at branch nodes (IQ-Tree/FastTree). Psychroserpens burtonensis DSM 12212 T (NZ_AUDE01000000.1) was used as the out-group. GenBank accession numbers of the whole genome sequences are shown in parentheses. Filled circles indicate branches that were recovered with both two methods (IQ-Tree and FastTree algorithms). Bar, 0.05 substitutions per nucleotide position
A Gram-stain-negative, orange, aerobic, non-motile, rod-shaped marine bacterium, designated as 2V75T, was isolated from the coastal sediment of Xiaoshi Island, Weihai, China. The strain 2V75T grew at 20–45 °C (optimum, 37 °C), from pH 7.0 to 9.0 (optimum, pH 7.0) and in the presence of 0.5–5% (w/v) NaCl (optimum, 3%). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain 2V75T was affiliated to the genus Robiginitalea and had the highest sequence similarity with R. biformata KCTC 12146T (93.7%). The ANI values between strain 2V75T and R. biformata KCTC 12146T were 72.6%, respectively. The DNA G + C content was 54.8 mol%. MK-6 was the only respiratory quinone. Based on the phenotypic, phylogenetic and chemotaxonomic data, strain 2V75T should be classified as a novel species in the genus Robiginitalea, for which the name Robiginitalea marina is proposed. The type strain is 2V75T (= KCTC 92035T = MCCC 1H00484T).
 
Maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showing the relationship between selected species of the genus Nocardiopsis. Actinomadura madurae DSM 43067T was used as an outgroup. Bootstrap percentages over 50% derived from 1000 replications are showed at the nodes. Dots indicate branches also recovered in the neighbor-joining and maximum-parsimony trees. Bar, 0.0100 substitutions per site
Phylogenetic tree based on whole genome sequences of HDS12T and related reference strains. Tree inferred with FastME 2.1.6.1 (Vincent et al. 2015) from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values > 60% from 100 replications, with an average branch support of 96.0%. The tree was rooted at the midpoint (Farris 1972)
A novel actinobacterium, designated strain HDS12T, was isolated from fruits collected from Changde city located in the northwest of Hunan Province, China and characterized using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that strain HDS12T belonged to the genus Nocardiopsis, and had highest similarities to N. dassonvillei subsp. dassonvillei CGMCC 4.1231T (99.79%), N. deserti H13T (99.73%), N. alborubida NBRC 13392T (99.66%), N. dassonvillei subsp. crassaminis D1T (99.64%), N. synnemataformans DSM 44143T (99.45%), N. lucentensis DSM 44048T (99.04%), N. aegyptia DSM 44442T (98.90%), N. flavescens CGMCC 4.5723T (98.76%), N. alba DSM 43377T (98.69%) and N. halotolerans DSM 44410T (98.63%), respectively. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain HDS12T formed an independent subclade, suggesting that strain HDS12T could belong to a potential novel species. Phylogenomic analysis demonstrated that strain HDS12T was closely related to N. dassonvillei subsp. dassonvillei CGMCC 4.1231T and N. dassonvillei subsp. crassaminis D1T. However, the average nucleotide identity value and the digital DNA-DNA hybridization value between them were well below 95–96% and 70% cut-off point recommended for delineating species. Based on its phenotypic and chemotaxonomic characteristics, strain HDS12T (= MCCC 1K06173T = JCM 34708T) represents the type strain of a novel species, for which the name Nocardiopsis akebiae sp. nov. is proposed.
 
We aimed to evaluate whether two commonly used PCR primers are effective to identify P. endodontalis and discriminate from other prevalent black-pigmented bacteria in apical periodontitis (AP). Endodontic canal samples from patients with asymptomatic AP (n = 20) were collected and cultured in anaerobiosis. Two primer sets to detect P. endodontalis were selected from the literature and first analyzed for their specificity in silico; and then tested on clinical isolates in vitro and finally, in apical exudates ex vivo. The identity of P. endodontalis was verified by PCR and Sanger sequencing with universal primers for bacterial V3–V6 regions 16S rDNA. Only one primer set showed specificity only for P. endodontalis clones in silico and also was specific for P. endodontalis in vitro and ex vivo.
 
Evolutionary relationships of taxa. Phylogenetic tree of 3 Actinobacterial strains and inferred from GBDP distances obtained with TYGS. It is constructed based on closely related species on 16S rRNA gene sequences, with the neighbor-joining method. T refers to the type of strain. Bootstrap values ≥ 90% are illustrated at branch nodes. Bar, 0.01 indicates nucleotide substitution rate
MTT cytotoxicity assay. It shows the percentage of A549 cell viability is concentration-dependent, a Doxorubicin and b, c, d the metabolites of three strains on the cell viability of the A549 lung cancer cell line after 48 h of incubation
Changes in the expression of bax and bcl-2 genes in A549 cells treated with the three metabolites of Actinomycetes isolates. Increased expression of the bax gene in cells treated with isolates 1 and 2 was significantly different from the control (P < 0.0008, P < 0.00056). However, increased expression of the bax gene in cells treated with isolate 3 did not show a significant difference compared to control. The difference in bcl-2 gene expression in cells treated with isolates 1 and 3 showed a significant decrease (P < 0.0006, P < 0.0004) compared to the control, but this difference in cells treated with isolate 2 did not show a significant decrease compared to the control. All tests were performed in triplicates and the data represent as mean ± SD. *P < 0.05; **P < 0.01; ***P < 0.001 are considered as significance
HPLC and GC–MS graphs of three selected isolates secondary metabolites. a HPLC. Anticancer compounds S. griseoflavus showed absorption peaks at retention times (min) of 16.724, 17.504, 20.641, and 21.811. Similarly, the antitumor compounds of S. calvus showed absorption peaks at retention times (min) of 16.724, 17.504, and 20.641. In addition, K. phosalacineus antitumor compounds showed absorption peaks at retention times (min) of 16.724, and 17.504. Peaks of 16.724, 17.504, 20.641, and 21.811 times had antitumor activity. b GC–MS Chromatographic analysis of total ethyl acetate extract with anticancer activity from three Actinomycetes isolates. aStreptomyces griseoflavus, and bStreptomyces calvus, and cKitasatospora phosalacineus
Flow cytometric analysis of apoptosis induction by three selected strains after incubation. a Control, bS. griseoflavus, cS. calvus, dK. phosalacineus. Dots represent viable intact cells with annexin V-/PI − (Q4), early apoptotic cells with annexin V + /PI − (Q1), dead late apoptotic cells with annexin V + /PI + (Q2), and necrotic cells annexin with V − /PI + (Q3) features
Actinomycetes are filamentous bacteria and the residents of the soil, prone to produce bioactive metabolites. This research aimed to isolate, classify, and investigate the anticancer properties of Actinomycetes secondary metabolites from various saline soils of Qom province. Actinomycetes isolates were molecularly recognized by 16SrRNA gene sequencing after the PCR procedure. The A549 cell line was then exposed to bacterial metabolites to find their cytotoxicity by MTT assay and their capacity to cause apoptosis by Flow cytometry. The expression levels of the bax and bcl-2 genes were determined using Real-time PCR. Bacterial metabolites were distinct by HPLC and GC–MS assays. Sequencing identified three novel Actinomycetes strains, Streptomyces griseoflavus, Streptomyces calvus, and Kitasatospora phosalacineus. The IC50 doses of bacterial metabolites were discovered equal to 1337, 2619, and 4874 µg/ml, respectively. Flow cytometric assay revealed that their secondary metabolites were capable of inducing apoptosis in A549 cells by 25%, 14.5%, and 7.58%, respectively. Real-time PCR findings displayed that the bax gene expression in A549 cells treated with S. griseoflavus and S. calvus, comparatively increased (P < 0.0008, P < 0.00056). The expression of the bcl-2 gene was significantly reduced in cells treated with S. griseoflavus and K. phosalacineus (P < 0.0006, P < 0.0004). The findings of this analysis showed the presence of new isolates in a soil sample from Qom province which can produce new anticancer agents and can be considered appropriate candidates for further research to employ as anticancer drugs.
 
Steps of experiment and examples of methods discussed in this review to investigate plant–microbe interaction within the root structure
A diverse lineage of microorganisms inhabits plant roots and interacts with plants in various ways. Further, these microbes communicate and interact with each other within the root microbial community. These symbioses add an array of influences, such as plant growth promotion or indirect protection to the host plant. Omics technology and genetic manipulation have been applied to unravel these interactions. Recent studies probed plants’ control over microbes. However, the activity of the root microbial community under host influence has not been elucidated enough. In this mini-review, we discussed the recent advances and limits of omics technology and genetics for dissecting the activity of the root-associated microbial community. These materials may help us formulate the correct experimental plans to capture the entire molecular mechanisms of the plant–microbe interaction.
 
Phylogenetic position of strain ASN36T, based on the 16S rRNA gene sequences. This maximum likelihood tree was constructed based on Kimura 2-parameter model. A discrete gamma distribution was used to model differences in evolutionary rates among sites (5 categories). The rate variation model allowed for some sites to be invariable (53.53% sites). All positions containing gaps and missing data were eliminated, leaving a total of 1,345 positions in the final data set. Numbers on nodes represent percentage values of 1,000 bootstrap resampling
A novel sulfate-reducing bacterium, strain ASN36T, was isolated from sediment of a brackish lake in Japan. Cells of strain ASN36T were not motile and rod-shaped, with length of 2.0–4.9 μm and width of 0.6–0.9 μm. Growth was observed at 5–35 °C with an optimum growth temperature of 25–30 °C. The pH range for growth was 6.6–8.8 with an optimum pH of 7.3. Major fatty acids were C16:1ω7c and C16:0. Under sulfate-reducing conditions, strain ASN36T utilized lactate, malate, pyruvate, butyrate, ethanol, butanol, glycerol, yeast extract and H2/CO2 as growth substrate. Fermentative growth occurred on malate and pyruvate. The novel isolate used sulfate, sulfite and thiosulfate as electron acceptors. The genome of strain ASN36T is composed of a chromosome with length of 6.3 Mbp and G + C content of 55.1 mol%. Analyses of the 16S rRNA gene indicated that strain ASN36T is related to Desulfoluna species. Overall genome relatedness indices indicated that strain ASN36T does not belong to any existing species. In contrast to the closest relatives, strain ASN36T lacks genes for reductive dehalogenase required for organohalide respiration and does not use halogenated aromatics as electron acceptors. On the basis of its genomic and phenotypic properties, strain ASN36T (= DSM 111985 T = JCM 39257 T) is proposed as the type strain of a new species, Desulfoluna limicola sp. nov.
 
Neighbour-joining tree based on 16S rRNA gene sequences, showing the phylogenetic position of strain PS1T and related members within the genus Pseudomonas. Solid circles indicate that the corresponding nodes (groupings) are also recovered in maximum-likelihood trees. Cellvibrio ostraviensis LMG 19434T (GenBank accession number: AJ493583) was used as an outgroup. Bootstrap values (expressed as percentages of 1000 replications) of above 50% are shown at the branch points. Bar, 0.01 substitutions per nucleotide position (MEGA X)
A novel marine Gram-stain-negative, aerobic, rod-shaped bacterium, designated as strain PS1 T , was isolated from the deep-sea sediments of the Mariana Trench and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 35 °C (ranging 10-45 °C), pH 6 (ranging pH 5-10) and with 11% (w/v) NaCl (ranging 0-17%). The 16S rRNA gene sequence similarity results revealed that strain PS1 T was most closely related to Pseudomonas stutzeri ATCC 17588 T , Pseudomonas nitrititolerans GL14 T , Pseudomonas zhaodongensis NEAU-ST5-21 T , Pseudomonas xanthomarina DSM 18231 T and Pseudomonas kunmingensis HL22-2 T with 98.3-98.7%. The digital DNA-DNA hybridization values and the average nucleotide identity between strain PS1 T and the reference strains were 20.4-40.1% and 78.7-79.4%, respectively. The major respiratory quinone is ubiquinone Q-9. The major polar lipids were phosphatidylethanolamine, diphosphatidyg-lycerol, phosphatidylglycerol, phosphatidylcholine, aminoglycolipid, two unidentified glycolipids and one unidentified lipid. The predominant cellular fatty acids of strain PS1 T were summed feature 8 (C 18:1 ω7c and/or C 18:1 ω6c), summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c), C 16:0 and cyclo-C 19:0 ω8c. The G + C content of the genomic DNA was 63.0%. The combined genotypic and phenotypic data indicated that strain PS1 T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas marianensis sp. nov. is proposed, with the type strain PS1 T (= DSM 112238 T = MCCC 1K05112 T).
 
The persistence of Staphylococcus aureus within biofilm can lead to contamination of medical devices and life-threatening infections. Luckily, lactic acid bacteria (LAB) have an inhibitory effect on the growth of these bacteria. This study aims to select LAB strains from fermented vegetables, and analyze their potential inhibition activities against S. aureus. In total, 45 isolates of LAB were successfully isolated from Sichuan pickles, and the CFS of Lactiplantibacillus plantarum LR-14 exerted the strongest inhibitory effect against S. aureus. Moreover, S. aureus cells in planktonic and biofilm states both wrinkled and damaged when treated with the CFS of L. plantarum LR-14. In addition, whole genome sequencing analysis indicates that L. plantarum LR-14 contains various functional genes, including predicted extracellular polysaccharides (EPS) biosynthesis genes, and genes participating in the synthesis and metabolism of fatty acid, implying that L. plantarum LR-14 has the potential to be used as a probiotic with multiple functions.
 
Phylogenetic tree generated using the complete genome sequence of K. paraultunense strain KD-1 based on GTDB database. Numbers in brackets indicated accession numbers for the genome sequences
Genes are classified by function. A Pathway annotation based on the KEGG database. B Functional annotation diagram based on the COG database
Sequence homology and conserved domain analysis of the potential keratinase and disulfide bond reductase of strain KD-1 and the enzymes identified by previous studies. a Keratinase; b Glutaredoxin; c Thioredoxin; d Thioredoxin reductase. Phylogenetic trees were constructed using Mega 7.0 with the neighbor-joining method according to amino acid sequences. Motif analysis was performed with the MEME web server. Up to ten conserved motifs were identified, with different motifs marked by different colored boxes. Each color block in the different proteins indicates a specific motif. Protein orientations are indicated (Nter–Cter) on the x-axis
Metabolic pathway map based on KEGG database. The black arrows in the metabolic pathway diagram represent the complete annotated metabolic pathways in the genome of strain KD-1. The dotted black arrows represent the metabolic pathways with complete annotation, but omit part of the intermediate transition processes. The dotted red arrows indicate that no genes associated with this metabolic pathway have been found in the genome
Keratinibaculum paraultunense strain KD-1 T (= JCM 18769 T = DSM 26752 T) is a strictly anaerobic rod-shaped bacterium. Under optimal conditions, feather keratin can be completely degraded by strain KD-1 within 24 h. Genomic sequencing showed that the genome was a single circular chromosome consisting of 2,307,997 base pairs (bp), with an average G + C content of 29.8% and no plasmids. A total of 2308 genes were annotated, accounting for 88.87% of the genomic sequence, and 1495 genes were functionally annotated. Among these, genes Kpa0144, Kpa0540, and Kpa0541 encoding the thioredoxin family members were identified, and may encode the potential disulfide reductases, with redox activity for protein disulfide bonds. Two potential keratinase-encoding genes, Kpa1675 and Kpa2139, were also identified, and corresponded to the ability of strain KD-1 to hydrolyze keratin. Strain KD-1 encoded genes involved in the heterotrophic metabolic pathways of 14 amino acids and various carbohydrates. The metabolic pathways for amino acid and carbohydrate metabolism were mapped in strain KD-1 based on KEGG annotations. The complete genome of strain KD-1 provided fundamental data for the further investigation of its physiology and genetics.
 
Phylogenetic tree based on genome sequences of Streptococcus ruminicola CNU_G2T, CNU_77-61, CNU_G3, and sixteen representative type strains of Streptococcus species and subspecies including SBSEC by Type (Strain) Genome Server (TYGS). The tree was constructed using the Genome-BLAST Distance Phylogeny (GBDP) with branch support of formulas D4, inferred from sum of all identities found in high-scoring pairs (HSPs) divided by total genome length. The three representative genomes used in this study are emphasized in bold
Heat maps representing the degree of similarity of Streptococcus ruminicola CNU_G2T, CNU_77-61, CNU_G3, and the SBSEC genome based on a the average nucleotide identity and b digital DNA–DNA hybridization (dDDH). The three representative genomes used in this study are emphasized in bold. Color intensity indicates ANI and dDDH values. Squares corresponding to values of less than 95 and 70% are colored in blue and values of more than 95 and 70% are indicated with red squares
A total of three Gram-positive, and oxidase and catalase-negative facultative anaerobic non-motile bacteria were isolated from the rumen fluid of cows and goats and these strains were designated CNU_G2T, CNU_77-61, and CNU_G3. They grew at 20–45 °C, pH 6.5–7, and 0–6.5% NaCl (w/v). The G + C contents (%) of the three isolates were 37.9, 37.8 and 37.8, respectively. Phylogenomic analysis indicated that these strains were distinct from other Streptococcus species. The average nucleotide identity between the isolates and the closest strain S. infantarius subsp. infantarius ATCC BAA-102T was 94.0–94.5%, while the digital DNA–DNA hybridization (dDDH) values between the isolates and the aforementioned related strain were 58.2–61.4%, respectively. Fatty acid analysis revealed higher proportions of C16:0 (> 28%) in all three isolates, while the proportion of C18:0 was higher in CNU_G2T (25.8%); however, it was less than 12% in all the representing strains used in the study. The C14:0 composition of strains CNU_77-61 (22.1%) and CNU_G3 (24.1%) was higher than that of type strains of CNU_G2T (8.1%). Based on the morphological, biochemical, and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus, for which we propose as Streptococcus ruminicola sp. nov. The type strain is CNU_G2T (= KCTC 43308T = GDMCC 1.2785T).
 
γ-Linolenic acid (GLA) is an essential n-6 polyunsaturated fatty acid (PUFA) that has received considerable attention in human and animal feed. GLA is used in many nutritional and medicinal applications, such as the treatment of cancer, inflammatory disorders, and diabetes. Currently, plant seed is the primary dietary source of GLA that is not enough to utilize on an industrial scale. To generate a sustainable novel source of GLA, the gene of delta-6 desaturase, one of the essential enzymes in the GLA production pathway, was isolated from Mucor rouxii DSM1194 and expressed in P. pastoris GS115 by pPICZC vector. The recombinant yeast expressed the GLA up to 19.2% (72 mg/g) of total fatty acids. GLA production of recombinant yeast was studied in a fermenter by oil waste for 5 days, and results detected 6.3 g/l lipid, and 103 mg/g GLA was produced in 72 h. The present study may provide an opportunity to develop an alternative host for manufacturing GLA on an industrial scale.
 
The Neighbour-joining tree of strain Q2-2 T and its related type genera constructed based on the 16S rRNA gene sequences, using the Kimura two-parameter model. Bootstrap values were based on 1000 replicates. The filled circles represent the same topological structures in the ML tree. Scale bar indicates 0.010 substitutions per nucleotide position
Neighbour-joining tree constructed based on tandem housekeeping genes (gyrB, hisS, recA, rpoB), showing the phylogenetic relationships of strain Q2-2 T and related strains. Bootstrap values were based on 1000 replicates. Scale bar indicates 0.050 substitutions per amino acid position
A urea-utilizing bacterium, designated Q2-2 T, was isolated from landfill. Cells of strain Q2-2 T were Gram stain-negative, aerobic, short-rod bacteria. Strain Q2-2 T was observed to grow at a temperature range of 15–37℃ (optimum 30 ℃), a pH range of 5.5–9.5 (optimum pH 8.0) and 0–4% (w/v) NaCl (optimum 1%). The major respiratory quinone was Q-8, and the major polar lipids were diphosphatidyl glycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, and phosphatidyl glycerol. Based on the 16S rRNA gene sequence, strain Q2-2 T had the highest similarity with Paracandidimonas caeni 24 T (98.0%), followed by Pusillimonas soli MJ07T (97.5%), Parapusillimonas granuli Ch07T (97.2%), Pusillimonas ginsengisoli DCY25T (97.1%) and Paracandidimonas soli IMT-305 T (96.4%). The ANI values between strain Q2-2 T and the above related type strains were 71.02%, 73.52%, 74.32%, 74.59% and 72.29%, respectively. The DNA G + C content of strain Q2-2 T was 61.1%. Therefore, strain Q2-2 T represents a novel species of the genus Paracandidimonas, for which the name Paracandidimonas lactea sp. nov. (type strain Q2-2 T = CGMCC 1.19179 T = JCM 34906 T) is proposed.
 
Chemical structures of the milbemcyins and physical map of their biosynthetic gene cluster. a Chemical structure of milbemycins. b Genetic organization of mil cluster in S. bingchenggensis. Arrows indicate separate ORFs. The PKS genes (milA1, milA2, milA3, milA4) encoding backbone synthases were showed in green. Yellow arrows for genes involved in tailoring steps. Red for the regulator gene and gray for genes with unknown function
Milbemycin production was affected by MilR3 in S. bingchenggensis TMB. a Milbemycin A3/A4 production in TMB/pSET152, DmilR3, CmilR3 and OmilR3 strains. b Picture of methanol extracts of fermentation broth of TMB/pSET152, DmilR3, CmilR3 and OmilR3 strains. c The growth phenotypes of TMB/pSET152, DmilR3, CmilR3 and OmilR3 strains grown on MS plates for 2, 4, 6 or 8 days
The type II PKS cluster was responsible for the yellow pigment biosynthesis in S. bingchenggensis TMB. a The growth phenotypes of TMB and Dsbi_06844 grown on MS plates at 7 days. b The UV–Vis spectrum absorption of methanol extractions of strains Dsbi_06844, DmilR3 and TMB/pSET152 fermentation culture. c Relative production of yellow pigment from strains DmiR3, Dsbi_06844, OmilR3 and TMB/pSET152 by optical density at 440 nm
The milbemycin biosynthesis was uncoupled with yellow pigment producing in S. bingchenggensis TMB. a Milbemycin A3/A4 production in TMB and Dsbi_06844 strains. b qRT-PCR analysis of sbi_06844 in TMB and Dsbi_06844 strain. c qRT-PCR analysis of milR in TMB and Dsbi_06844 strain. d qRT-PCR analysis of milR3 in TMB and Dsbi_06844 strain. All RNA samples were isolated from fermentation culture broth of TMB and Dsbi_06844 at 2, 4, 6 and 8 days, respectively. The relative transcriptional levels of each gene are calibrated with its transcription in TMB at 2 days
MilR3 regulated transcription of genes involved in milbemycin and yellow pigment biosynthesis. amilA2. bmilA4. cmilD. dmilR. esbi_06844. fmilR2. The relative transcription levels of these genes were compared among TMB/pSET152, DmilR3, CmilR3 and OmilR3 strains and represented separately. RNA samples were isolated from fermentation culture broth of TMB/pSET152, DmilR3, CmilR3 and OmilR3 at 2, 4, 6 and 8 days
Streptomyces bingchenggensis is the main industrial producer of milbemycins, which are a group of 16-membered macrocylic lactones with excellent insecticidal activities. In the past several decades, scientists have made great efforts to solve its low productivity. However, a lack of understanding of the regulatory network of milbemycin biosynthesis limited the development of high-producing strains using a regulatory rewiring strategy. SARPs (Streptomyces Antibiotic Regulatory Proteins) family regulators are widely distributed and play key roles in regulating antibiotics production in actinobacteria. In this paper, MilR3 (encoded by sbi_06842) has been screened out for significantly affecting milbemycin production from all the 19 putative SARP family regulators in S. bingchenggensis with the DNase-deactivated Cpf1-based integrative CRISPRi system. Interestingly, milR3 is about 7 Mb away from milbemycin biosynthetic gene cluster and adjacent to a putative type II PKS (the core minimal PKS encoding genes are sbi_06843, sbi_06844, sbi_06845 and sbi_06846) gene cluster, which was proved to be responsible for producing a yellow pigment. The quantitative real-time PCR analysis proved that MilR3 positively affected the transcription of specific genes within milbemycin BGC and those from the type II PKS gene cluster. Unlike previous “small” SARP family regulators that played pathway-specific roles, MilR3 was probably a unique SARP family regulator and played a pleotropic role. MilR3 was an upper level regulator in the MilR3-MilR regulatory cascade. This study first illustrated the co-regulatory role of this unique SARP regulator. This greatly enriches our understanding of SARPs and lay a solid foundation for milbemycin yield enhancement in the near future.
 
Growth of isolates in the presence of Fe³⁺. Isolates Azospira oryzae 6a3 and Cupriavidus metallidurans CH34 were cultured at 16 mmol l⁻¹ Fe³⁺. Isolates Enterobacter bugandensis EB-247 was cultured at 27 mmol l⁻¹. Isolates Citrobacter freundii ATCC 8090 and Citrobacter murliniae CDC2970-59 were cultured at 55 mmol l⁻¹ Fe³⁺. Acetate was the source of carbon for all isolates. Data presented are average ± standard deviation of triplicates
Scheme of a proposal for iron reduction and acetate oxidation mediated by electrogenic bacteria cultured in these experiments
Final Fe²⁺ concentrations and percentage of Fe³⁺ reduction by planktonic cells (anolyte) at three different concentrations of Fe³⁺ and different proportions of the initial inoculum. In black 16 mmol l⁻¹ Fe³⁺, in blue 27 mmol l⁻¹ Fe³⁺, in red 55 mmol l⁻¹ Fe³⁺. Acetate was the source of carbon for all cultures. Data presented are average ± standard deviation of triplicates
Cultures of the planktonic cells (anolyte) at three different concentrations of Fe³⁺ (16, 27 and 55 mmol l⁻¹) and different proportions of initial inoculum (5, 10, 20 and 30% (v/v). Left, initial cultures; right cultures after 4 days
In this study, bacteria from a microbial fuel cell (MFC) and isolates were evaluated on their Fe3+ reduction capability at different concentrations of iron using acetate as the sole source of carbon. The results demonstrated that the planktonic cells can reach an iron reduction up to 60% at 27 mmol Fe3+. Azospira oryzae (µ 0.89 ± 0.27 d-1) and Cupriavidus metallidurans CH34 (µ 2.34 ± 0.81 d-1) presented 55 and 62% of Fe3+ reduction respectively at 16 mmol l-1. Enterobacter bugandensis (µ 0.4 ± 0.01 d-1) 40% Fe3+ at 27 mmol l-1, Citrobacter freundii ATCC 8090 (µ 0.23 ± 0.05 d-1) and Citrobacter murliniae CDC2970-59 ( µ 0.34 ± 0.02 d-1) reduced Fe3+ in ~50 %, at 55 mmol l-1. This is the first report on these bacteria on percentage of iron reduction. These results may be useful for anode design to contribute to a higher energy generation in MFCs.
 
Maximum-likelihood tree showing the phylogenetic position of strain JJ-42 T among the closest related Paenibacillus species. The tree was generated in ARB using RAxML (GTR-GAMMA, rapid bootstrap analysis) and based on the 16S rRNA gene sequences between positions 95–1475 according to E. coli numbering (Brosius et al. 1978). GenBank/EMBL/DDBJ accession numbers are given in parentheses. Numbers at branch nodes refer to bootstrap values > 70% (100 replicates). Circle marks nodes that were also present in the maximum-parsimony tree. Larger circles were supported by high bootstrap values in the maximum-parsimony tree. Type strains of Cohnella species were used as outgroup. Bar, 0.1 substitutions per nucleotide position
Whole-genome-based tree showing the phylogenetic placement of strain JJ-42 T among type strains of closely related Paenibacillus species. This minimum evolution tree was inferred using JolyTree (https://gitlab.pasteur.fr/GIPhy/JolyTree). Two publicly available Cohnella type strain genomes were used as an outgroup. The genome sequence accession is specified between parentheses next after each taxon name. Branch supports were assessed by the rate of elementary quartets, as estimated by JolyTree (only supports > 0.5 were specified). Bar, 0.025 nucleotide substitutions per site
A Gram-positive staining, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays was studied for its detailed taxonomic allocation. Based on the 16S rRNA gene sequence similarity comparisons, strain JJ-42 T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus pectinilyticus (98.8%). The 16S rRNA gene sequence similarity to all other Paenibacillus species was below 98.5%. The pairwise average nucleotide identity (ANI) and digital DNA−DNA hybridization (dDDH) values of the JJ-42 T genome assembly against publicly available Paenibacillus type strain genomes were below 92% and 47%, respectively. The quinone system of strain JJ-42 T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three aminophospholipids (APL), and one unidentified lipid. The major fatty acids were iso- and anteiso-branched with the major compound anteiso C15:0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-42 T from the most closely related species. Thus, JJ-42 T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizoplanae sp. nov. is proposed, with JJ-42 T (= LMG 32089 T = CCM 9085 T = DSM 111786 T = CIP 111891 T) as the type strain.
 
This work aims at exploring an antagonistic actinobacterial strain isolated from the roots of Ziziphus lotus in bioformulation processes and the biocontrol of Rhizoctonia solani damping-off of tomato seedlings. The strain Streptomyces caeruleatus ZL-2 was investigated for the principal in vitro biocontrol mechanisms and then formulated in three different biofungicides: wettable talcum powder (WTP), sodium alginate propagules (SAP) and clay sodium alginate propagules (CAP). Compared to a marketed control products (Serenade® and Acil 060FS®), the formulated biofungicides were investigated against the R. solani damping-off of tomato cv. Aïcha seedlings. The strain ZL-2 produced chitinases, cellulases, β-1,3-glucanases, cyanhydric acid and siderophores. It also showed strong antagonistic effect on the mycelial growth of R. solani. Bioautographic and HPLC analysis revealed the production of a single or several co-migrating antifungal compounds. The biofungicide WTP presented an attractive biocontrol effect by significantly reducing the disease severity index (DSI) compared to untreated seeds. No significant differences were obtained compared to the chemical treatment with Acil 060FS®. The viability of spores and biocontrol efficacy of the WTP were confirmed after 1-year storage. Strain ZL-2 has never been reported in the bioformulation of active biofungicides against Rhizoctonia solani damping-off and this work opens up very attractive prospects in the fields of biocontrol and crop improvement.
 
Although Escherichia coli has four hydrogenases, their definite roles in fermentation are still not clear. In this study, all the operon deletion mutants of E.coli hydrogenases (∆hya, ∆hyb, ∆hyc, or ∆hyf) were constructed to evaluate the hydrogen metabolism in comparison to their respective single-gene deletion mutants of large subunits (∆hyaB, ∆hybC, ∆hycE, and ∆hyfG). Besides the hyc operon mutant that expectedly showed no hydrogen synthesis, the hyb operon mutant showed low hydrogen production and demonstrated significantly reduced growth under anaerobic conditions. The present work also provided first-hand data where deleterious effects of operon deletion were compared with single-gene deletion mutations and the results showed that the former type of deletion was found to cause more prominent phenotypic effects than the latter one. Interestingly, hyb operon mutant was remarkably distinct from other operon mutants, specifically in its inability to utilize glucose under both aerobic and anaerobic conditions. Further studies on this mutant revealed a significant reduction of the total intracellular ATP and NADH concentrations, which could explain its impaired glucose metabolism. In this way, Hyd-2 was verified as crucial not only in glucose metabolism but also in energy balance and redox homeostasis of the cells. Furthermore, a decreased expression of glucose metabolism-associated genes, particularly ppc and pykA, indicated their regulation by hyb operon, and thereby, glucose consumption. Moreover, the transcriptional changes in this mutant indicated the wide genomic connectivity of hyb operon to other metabolisms.
 
Microplastic is a minute particle of chemical pollutant in marine environment and classified as less than 5 mm size. The microplastics could not degrade for long years and they are ingested, incorporated, and accumulated in tissues of living organisms, particularly can cause various ecotoxicological effects for their behavioural change, cytotoxicity, neuro-toxicity effects, liver stress, etc. This preliminary study was investigated the abundance and accumulation of microplastic in marine fish of Indian mackerel (Rastrelliger kanagurta) gut region. Further, we identified the microplastic through stereomicroscope in Indian mackerel fish size up to 0.02 mm. In FT-IR analysis were identified the chemical group which were represents as nylon. In GC–MS analysis were identified that hexa decanoic acid and methyl ester plastic compounds as well as identify and screened the microplastic degrading bacteria from fish gut through partial 16S rRNA gene sequencing analysis it was shows that the isolate reveals a Pseudomonas sp. As a result, it is possible that gut bacteria have a probiotic role in fish gut to may degrade microplastics.
 
Spontaneous production of E colicins is known to occur in only a small fraction of colicinogenic population. The current study aimed to determine if the same holds true for the production of colicin E9 in real time, by investigating the induction dynamics of the promoter of the ColE9 operon which results in the expression of the ColE9 activity and functional genes. A novel fluorescent reporter was constructed which carries the fusion of the ColE9 promoter and the gfpmut2 gene in a low copy number plasmid that was compatible with the native ColE9-J plasmid. Using the fluorescent reporter construct in the non colicinogenic E. coli cells, the induction of the ColE9 promoter was investigated. The current study demonstrates that the spontaneous induction of the ColE9 promoter occurs in a heterogenous manner and this heterogeneity is maintained in a bacterial population for several generations suggesting that it is unlikely due to any irreversible mutation in the bacterial culture. Furthermore, the same investigations were repeated using the colicin E9 producing E. coli cells. Flow cytometry analysis revealed that 7.1 ± 0.68% of the colicin E9 producing E. coli cells expressed GFP albeit only 2.45 ± 0.30% was observed from non colicinogenic E. coli cells. The considerable increase in the number of the fluorescent cells was likely due to the DNase activity of colicin E9 produced by their clonemates, resulting the auto-induction, which can be abolished with the inactivation of the DNase activity of the colicin E9.
 
The present study described the cytopathic effect of PPR virus presently being used in serial passages at the level of 60th in Vero cells and infected tissue culture fluid was used in this study as viral inoculum. Vero cells were grown on cover slip & were infected with tissue culture fluid at a fixed multiplicity of infection (MOI) 0.01. The infected cover slip along with control were stained with H&E stain at periodic intervals and cytopathic effect was studied with microscope. The cytopathic effect (CPE) was visible at first from 24 hpi and the Vero cells showed initial cell rounding, aggregation, and syncytial development. Development of inclusion bodies and cell degradation was noticed by 72 hpi. Complete detachment of the cell monolayer was observed by 84 hpi. It is concluded that, development of numerous inclusion bodies are the indication of well adaptation & extensive multiplication of PPRV in Vero cells.
 
The effects of low (a) and high (b) pH on the growth of selected Lactobacillus isolates
The effects of NaCl (a) and bile salt (b) on selected Lactobacillus isolate (C1) growth
The blast of the 23S rRNA gene sequence of C1 strain (lacto.C1 (SRX11028965)). The results of blast showed 100% identity of C1 sequence with ZT-LpI.34 strain.*Accession number
The effects of selected Lactobacillus plantarum strain (a, b) and nanochitosan (c, d) on standard and extracted AFB1 concentration in medium. e, f the synergistic effects of selected Lactobacillus plantarum strain and nanochitosan on standard and extracted AFB1, respectively
The present study aimed to evaluate the effects of new Lactobacillus plantarum strain isolated from dairy products as well as chitosan nanoparticles on reducing aflatoxin B1 (AFB1) toxicity In vitro. After collection and preparation of yogurt, cheese, milk, and whey products, lactic acid bacteria (LABs) were isolated and identified using biochemical and molecular methods. pH, bile, and salt tolerance tests were used to measure probiotic activity. Then, the antimicrobial activity of LABs against gastrointestinal pathogens was studied. The strain isolated from cheese (C1) was selected as the appropriate strain and antibiotic susceptibility test was performed for this strain. Then, the effect of C1 isolate and chitosan nanoparticles on reducing aflatoxin B1 (AFB1) in the medium was studied by measuring AFB1 using the enzyme-linked immunosorbent assay (ELISA) and high-performance liquid chromatography (HPLC). The results of biochemical evaluations indicated the separation of different strains of L. plantarum. Antimicrobial activity test showed extensive antimicrobial activity of C1 isolate. The results showed that this strain has good probiotic activities. This strain was shown to be resistant to erythromycin, fusidic acid, gentamicin, kanamycin, nalidixic acid, neomycin, ofloxacin, and vancomycin antibiotics. C1 strain together with chitosan nanoparticles was able to reduce AFB1 in the medium and, when both were used simultaneously, a synergistic effect was seen in reducing AFB1 from the medium. Based on the findings, it can be concluded that the new C1 L. plantarum strains together with chitosan nanoparticles had synergistic effects on reducing AFB1 toxin in food products.
 
Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the positions of Devosia litorisediminis BSSL-BM10T, the type strains of Devosia species and representatives of some other related taxa. Only bootstrap values greater than 50% are shown at branching points. Filled circles indicate that the corresponding nodes were also recovered in the trees generated with the maximum-likelihood and maximum-parsimony algorithms. Stappia stellulata IAM 12621T was used as an outgroup. Bar 0 0.01 substitutions per nucleotide position
A Gram-negative, aerobic, non-motile, and rod-shaped bacterial strain, designated BSSL-BM10T, was isolated from sand of a dune that was collected from the Yellow Sea, Republic of Korea. It was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis showed that strain BSSL-BM10T fell phylogenetically within the radiation comprising type strains of Devosia species. The 16S rRNA gene sequence of strain BSSL-BM10T shared sequence similarities of 98.2% with the type strain of D. naphthalenivorans and 93.5–97.7% with type strains of other Devosia species. ANI and dDDH values between strain BSSL-BM10T and type strains of 18 Devosia species were 71.0–78.4% and 18.8–21.5%, respectively. The DNA G + C content of strain BSSL-BM10T was 60.9% based on its genomic sequence data. Strain BSSL-BM10T contained Q-10 as the predominant ubiquinone and 11-methyl C18:1ω7c, C18:1ω7c, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and C16:0 as its major fatty acids. Major polar lipids of strain BSSL-BM10T were phosphatidylglycerol and two unidentified glycolipids. Strain BSSL-BM10T showed distinguishable phenotypic properties with its phylogenetic and genetic distinctiveness separated from recognized Devosia species. Based on data presented in this study, strain BSSL-BM10T should be placed in the genus Devosia. The name Devosia litorisediminis sp. nov. is proposed for strain BSSL-BM10T (= KACC 21633T = NBRC 115152T).
 
The sudden emergence of the SARS-CoV-2 Omicron variant is causing major global concern due to its high number of mutations compared to previous variants, which is a relatively rare but significant event that can change the course of viral evolution, the occurrence of which might have huge consequences for the natural evolution of species in general, prompting us to rethink our knowledge on evolution.
 
Kinetic experimental data (symbols) of E. coli, S. Enteritidis, L. monocytogenes, S. aureus, L. mesenteroides, and W. viridescens in the control samples (without addition of C. blanchetianus essential oil—CBEO, unfilled symbols) and in samples with different concentrations of C. blanchetianus essential oil (CBEO, filled symbols), and the fitting (continuous lines) of the Baranyi and Roberts growth and Weibull inactivation primary models. Filled symbols: squares, diamonds, triangles, and circles represent samples with 0.9 mg/mL, 1.8 mg/mL, 2.71 mg/mL, and 4.51 mg/mL of CBEO, respectively
δ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\delta$$\end{document} parameter values (symbols) of L. mesenteroides, L. monocytogenes, S. aureus, and W. viridescens at different concentrations (0.9–4.51 mg/mL) of C. blanchetianus essential oil (CBEO), and the fitting (continuous lines) of the power and hyperbolic secondary models
This study aimed to evaluate and model the antimicrobial action of different concentrations of Croton blanchetianus essential oil (CBEO) on the behavior of six bacterial species in vitro. CBEO extraction was performed by hydrodistillation and characterized by CG-MS. CBEO solutions in culture media were tested at 0.90, 1.80, 2.71, and 4.51 mg of CBEO/mL, against foodborne bacteria: pathogenic bacteria (Staphylococcus aureus, Listeria monocytogenes and Salmonella Enteritidis at 35 °C), a non-pathogenic Escherichia coli (at 35 °C), and spoilage bacteria (Weissella viridescens and Leuconostoc mesenteroides at 30 °C). The CBEO major compounds were eucalyptol, α-pinene, sativene, E-caryophyllene, bicyclogermacrene, and spatulenol. Baranyi and Roberts (growth) and Weibull (inactivation) primary models, along with power and hyperbolic secondary models, were able to describe the data. CBEO inactivated L. monocytogenes, S. aureus, L. mesenteroides and W. viridescens at all applied concentrations. CBEO did not inactivate S. Enteritidis and E. coli, but their growth rates were reduced.
 
The biogenic method for synthesis of nanoparticles is preferred over the traditional strategies, on account of its ease, environmental friendliness, and cost-effectivity, wherein fungi endorse themselves to be the most appropriate precursor for the same. In recent times numerous metal nanoparticles have been reported to exhibit significant therapeutic activities, out of which Zinc Oxide nanoparticles (ZnO NPs) stand apart on account of their multidimensional nature. Thus, this study was carried out with an aim to biosynthesize ZnO NPs utilizing endophyte Trichoderma viride, isolated from the seeds of Momordica charantia. The physicochemical characterization of NPs was done via employing a combination of spectroscopic and microscopic techniques. The NPs were found to have a hexagonal shape and possessed an average particle size of around 63.3 nm. The antimicrobial activity of NPs was evaluated against multi-drug resistant organisms and it was observed to be an appreciable one whereas the antioxidant activity was deduced to be dose-dependent. Thus, these ZnO NPs can be considered as a probable active ingredient of any future therapeutic conceptualization after undertaking a thorough toxicological assessment.
 
Antimicrobial activity of cell-free supernatant of isolates against pathogens, A Bacterial isolates of goat milk, B Bacterial isolates of sheep milk
The phylogenetic analysis was computed using the maximum composite likelihood method using MEGA 11 version. All the strains selected for evolutionary analysis were type strains except our isolates (E. faecium GMB24 and E. hirae SMB16)
Comparative analysis of goat and sheep milk isolates by A Principle component analysis, B Heatmsap analysis of survivability
Probiotic attributes of lactic acid bacteria isolated from goat and sheep milk samples were analysed by culturing them on an MRS agar medium. The most potential isolates, GMB24 and SMB16, were identified by biochemical tests which had ability to tolerate different concentrations of acid and bile and phenol resistance. They were further identified as Enterococcus faecium GMB24 and Enterococcus hirae SMB16 by 16S rRNA gene sequencing approach. The probiotic potential of the isolates GMB24 and SMB16 were recorded including antimicrobial activity against pathogenic bacteria viz., Escherichia coli (MTCC118), Staphylococcus aureus (MTCC7443), Pseudomonas aeruginosa (MTCC424), Listeria monocytogens (MTCC657) and Salmonella typhimurium (MTCC733), and antibiotic susceptibility test. The isolates SMB16 and GMB24 exhibited a higher zone of inhibition against P. aeruginosa (19.00 ± 0.57 mm) and S. aureus (25.66 ± 0.88 mm), respectively. The data from these experiments were used for the principal component analysis (PCA) to assess the survivability of the isolates under different factors. The heatmap generated in this study clustered the bacterial isolates based on their phenotype properties. Further, immunomodulating activities of these probiotic bacteria were tested on neutrophil adhesion test, haemagglutinating antibody titer and delayed-type hypersensitivity. Probiotic E. faecium GMB24 and E. hirae SMB16, at 109 cells/mL doses per day, increased the neutrophil adhesion, haemagglutinating antibody titer and DTH in comparison to the untreated control group. The isolates showed negative test for haemolytic and gelatinase activities and hence were considered safe. E. faecium GMB24 and E. hirae SMB16 were shown to have high probiotic potential and immune-stimulant action.
 
CgtA, a highly conserved 50S ribosome-associated essential GTPase, acts as a repressor of the stringent stress response under nutrient-rich growth conditions to suppress basal levels of the alarmone ppGpp in V. cholerae. To further explore the in vivo functionality of CgtA, we introduced an amino acid substitution, i.e., Gly98Asp, in a conserved glycine residue in the N-terminal domain. The constructed V. cholerae mutant was designated CgtA(G98D). Comparison of cell sizes of the CgtA(G98D)mutant with its isogenic wild-type (Wt) strain N16961 under different phases of growth by Transmission Electron Microscopy (TEM) and statistical analysis suggests that CgtA may control the cell size of V. cholerae. The cell length is significantly reduced, corresponding to the delayed growth in the mid-logarithmic phase. The differences in the cell length of CgtA(G98D) and Wt are indistinguishable in the late logarithmic phase. During the stationary phase, marked by higher OD600, a sub-population of CgtA(G98D) cells outnumbered the Wt cells lengthwise. CgtA(G98D) cells appeared slenderer than Wt cells with significantly reduced cell width. However, the centerline curvature is preserved in CgtA(G98D) cells. We propose that in addition to its multitude of intracellular roles, CgtA may influence the cell size of V. cholerae.
 
For sustainable production of cultured meat, we propose a novel circular cell culture (CCC) system in which microalgae are used as nutrient supply for the mammalian cell culture and as a waste-medium recycler. Chlorococcum littorale, RL34 hepatocytes, and C2C12 myoblasts were used as cell sources for microalgae, growth factor-producing cells, and muscle cells, respectively. In the first cycle, C2C12 cells were amplified 4.0-fold after 48 h of culture in an RL34 cell-conditioned medium. In the second cycle, C2C12 cells were cultured in the C. littorale culture waste medium to which the C. littorale-derived nutrients were added. The proliferation rates of C. littorale and C2C12 and the nutrient extraction efficiency from C. littorale were the same in the first and second cycles. Therefore, this CCC system, which works without additional grain-derived nutrients and animal sera, will help drastically reduce environmental load, resource/energy consumption, and costs in future cultured meat production.
 
Ehrlichia canis has gained importance over the years as a zoonotic bacterium, nevertheless in Mexico is unknown the extent of the problem in animals and public health. The country had a few studies carried out locally using serology and molecular tests as diagnostic methods. Ehrlichiosis is not considered endemic in the central valley of Mexico, because the climatic conditions in the region have not allowed the vector (Rhipicephalus sanguineus) to establish itself adequately, therefore, diagnosis is not used in clinical practice in this area. A nested PCR (nPCR) offers rapid results with high sensitivity and specificity regardless of cost. The use of a recombinant positive control provides the advantage of timely diagnosis, follow-up treatment and allows the clinician to decide. In this work, the nPCR reported by Wen et al. (J Clin Microbiol 35(7):1852-2185, 1997) was used for the diagnosis of E. canis by modifying the reaction conditions to improve the detection of the test. We constructed a recombinant positive control to nPCR as diagnostic technique for E. canis, also we modified the reaction conditions to improve detection of the test which allowed the diagnosis of E. canis in dogs in the Mexican Republic using 53 samples from dogs with positive serological diagnosis of Ehrlichiosis, some of them from the valley of Mexico. Currently, this nPCR is offered to public at the Faculty of Veterinary Medicine and Zootechnics of the National Autonomous University of Mexico at an accessible cost and allows to begin to generate epidemiological information to know distribution of the bacterium.
 
Neighbor-joining (NJ) tree constructed based on 16S rRNA gene sequences available from the GenBank database. Bootstrap values (expressed as percentages of 1000 replications) greater than 50% are shown at branch points. Bar, 0.01 represents substitutions per nucleotide position. Paenibacillus polymyxa DSM 36T used as the outgroup
Phylogenetic tree based on whole-genome sequences of A. kamchatkensis DSM 14988T and A. ayderensis AB04T and related reference strains. The tree was inferred with FastME 2.1.6.1 (Lefort et al. 2015) from genome blast distance phylogeny (GBDP) distances calculated from genome sequences using the TYGS server (https://tygs.dsmz.de) (Meier-Kolthoff and Göker 2019) The branch lengths are scaled in terms of GBDP distance formula d5. The numbers at branches are GBDP pseudo-bootstrap support values ≥ 64% from 100 replications with an average branch support of 97.7%. The tree was rooted at the midpoint (Farris, 1972)
Two-dimensional thin-layer chromatogram of polar lipids of AA. kamchatkensis DSM 14988T and BA. ayderensis AB04T. DPG diphosphatidylglycerol; PG phosphatidylglycerol; PE phosphatidylethanolamine; PC phosphatidylcholine; APL unidentified aminophospholipid; PL unidentified phospholipid
In this study, we aimed to clarify the taxonomic positions of Anoxybacilluskamchatkensis DSM 14988T and Anoxybacillusayderensis AB04T using whole-genome phylogenetic analysis, biochemical and chemotaxonomic characteristics. In phylogenetic trees drawn using whole-genome sequences and 16S rRNA gene sequences, A. kamchatkensis DSM 14988T and A. ayderensis AB04T clade together and showed high sequence similarity (99.6%) based on 16S rRNA gene. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between A. kamchatkensis DSM 14988T and A. ayderensis AB04T were found to be greater than the threshold values for species demarcation. Most phenotypic and chemotaxonomic features between both species were almost identical except for a few exceptions. The present results show that A. kamchatkensis DSM 14988T is a later heterotypic synonym of A. ayderensis AB04T.
 
An integrated approach involving vermicompost, chromate reducing bacteria and AMF was tested to manage the toxic impacts of Cr(VI) on Ocimum basilicum as a model plant. Pot experiments were conducted on O. basilicum plants in an artificially Cr(VI)-contaminated soil in two phases of experiment as bioinoculants experiment and vermicompost experiment. In the first phase of the bioinoculants experiment the series of gradient concentrations of Cr(VI) (0, 25, 50 and 100 mg kg–1 in soil) were evaluated with previously isolated four efficient Cr(VI)-reducing rhizo-bacterial strains (Bacillus Cereus strain SUCR 44, BC; Microbacterium sp. strain SUCR 140, MB; Bacillus thuringiensis strain SUCR186, BT; and Bacillus subtilis strain SUCR188; BS) along with Arbuscular Mycorrhizal Fungus—Glomus fasciculatum (GF) in alone and in co-inoculation form. In the second experiment (vermicompost) the best performing strain (MB) was tested alone or in combination with GF along with different doses of vermicompost. It was observed that vermicompost by itself could be useful in decreasing the bioavailable Cr(VI), uptake of Cr besides improving the nutritional status of plants. The vermicompost also played an important and indirect role and improved herb yield by supporting the multiplication of MB (Microbacterium sp.), an efficient chromate reducing rhizobacteria, that further decreased the bioavailable and toxic form of Cr and improved population and colonization of GF too. The translocation of Cr(VI) was averted through improved colonization of GF, also prevented higher accumulation of Cr in aerial parts (leafy herb) of O. basilicum.
 
Top-cited authors
Hans-Peter Klenk
  • Newcastle University
Cathrin Spröer
  • Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Jan P. Meier-Kolthoff
  • Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Sajid Nadeem
  • University of Agriculture Faisalabad
Muhammad Naveed
  • University of Agriculture Faisalabad