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Gut Microbes 2023Although changes in gut microbiome have been associated with the development of T2D and its complications, the role of the gut virome remains largely unknown. Here, we...
Although changes in gut microbiome have been associated with the development of T2D and its complications, the role of the gut virome remains largely unknown. Here, we characterized the gut virome alterations in T2D and its complications diabetic nephropathy (DN) by metagenomic sequencing of fecal viral-like particles. Compared with controls, T2D subjects, especially those with DN, had significantly lower viral richness and diversity. 81 viral species were identified to be significantly altered in T2D subjects, including a decrease in some phages (e.g. and ). DN subjects were depleted of 12 viral species, including , and , and enriched in 2 phages ( and ). Multiple viral functions, particularly those of phage lysing host bacteria, were markedly reduced in T2D and DN. Strong viral-bacterial interactions in healthy controls were disrupted in both T2D and DN. Moreover, the combined use of gut viral and bacterial markers achieved a powerful diagnostic performance for T2D and DN, with AUC of 99.03% and 98.19%, respectively. Our results suggest that T2D and its complication DN are characterized by a significant decrease in gut viral diversity, changes in specific virus species, loss of multiple viral functions, and disruption of viral-bacterial correlations. The combined gut viral and bacterial markers have diagnostic potential for T2D and DN.
Topics: Humans; Gastrointestinal Microbiome; Diabetic Nephropathies; Virome; Diabetes Mellitus, Type 2; Bacteriophages; Bacteria
PubMed: 37349979
DOI: 10.1080/19490976.2023.2226925 -
Frontiers in Chemistry 2022Natural products derived from microorganisms play a prominent role in drug discovery as potential anti-infective agents. Over the past few decades, lipopeptides produced... (Review)
Review
Natural products derived from microorganisms play a prominent role in drug discovery as potential anti-infective agents. Over the past few decades, lipopeptides produced by particularly , , , and cyanobacteria species, have been extensively studied for their antimicrobial potential. Subsequently, daptomycin and polymyxin B were approved by the Food and Drug Administration as lipopeptide antibiotics. Recent studies have however, indicated that , and , as well as predatory bacteria such as , and , hold promise as relatively underexplored sources of novel classes of lipopeptides. This review will thus highlight the structures and the newly discovered scaffolds of lipopeptide families produced by these bacterial genera, with potential antimicrobial activities. Additionally, insight into the mode of action and biosynthesis of these lipopeptides will be provided and the application of a genome mining approach, to ascertain the biosynthetic gene cluster potential of these bacterial genera (genomes available on the National Center for Biotechnology Information) for their future pharmaceutical exploitation, will be discussed.
PubMed: 36277345
DOI: 10.3389/fchem.2022.1025979 -
Journal, Genetic Engineering &... Feb 2023Applying microbial biostimulants during crop cultivation allows for higher sustainability levels. It reduces the need for fertilizers and environmental contaminants...
BACKGROUND
Applying microbial biostimulants during crop cultivation allows for higher sustainability levels. It reduces the need for fertilizers and environmental contaminants while enhancing plant quality. This study assessed 13 endophytic bacteria, 4 newly isolated, and 9 donated, for plant growth-promoting capabilities. Quantitative assessments of indole acetic acid (IAA), gibberellic acid (GA), siderophores, ammonia, exopolysaccharides, volatile HCN, and phosphate solubilization, along with Bray-Curtis cluster analyses were performed.
RESULTS
Upon the results we selected RhizobiumMAP7, Brevibacillus DesertYSK, Pseudomonas MAP8, BacillusMAP3, Brevibacillus MAP, and Bacillus DeltaYSK to evaluate their effects on Lactuca sativa growth and pigmentation in a 30-day greenhouse pot experiment. Both Brevibacillus DesertYSK and Rhizobium MAP7surpassed other strains in growth promotional effects. They doubled shoot length (12 and 12.3 cm, respectively, when compared with 7 cm for control after 30 days), and fresh weight (0.079 and 0.084 g, respectively, when compared with 0.045 g for control after 30 days), and increased root length by at least 3-fold when compared with control (4.5 and 3.5 cm, respectively, when compared with 1.2 cm for control after 30 days). Chlorophyll content also exhibited at least a 2-fold significant increase in response to bacterization compared with control.
CONCLUSIONS
This strain superiority was consistent with the in vitro assays data that showed strains capability as IAA and GAproducers. Also, strains were highly capable ammonia and siderophore producers and phosphate solubilizers, providing considerable hormone and nutrient levels for L. sativa plantsleading to improved growth parameters and appearance. These data support the notion that nodule-based bacteria are potential plant growth-promoting bacteria (PGPB) that may be used on a wider scale rather than just for legumes.
PubMed: 36780046
DOI: 10.1186/s43141-023-00465-1 -
Microorganisms May 2021Sixteen strains of five genera of thermophilic bacteria, i.e., , and were cultivated at a temperature from 42 to 70 °C. Twelve strains were obtained from the Czech...
Sixteen strains of five genera of thermophilic bacteria, i.e., , and were cultivated at a temperature from 42 to 70 °C. Twelve strains were obtained from the Czech Collection of Microorganisms, while four were directly isolated and identified by 16S rRNA gene sequencing from the hot springs of the world-famous Carlsbad spa (Czech Republic). Polyprenol homologs from C40 to C65 as well as free undecaprenol (C55), undecaprenyl phosphate, and undecaprenyl diphosphate were identified by shotgun analysis and RP-HPLC/MS-ESI (reverse phase high-performance liquid chromatography-high-resolution positive electrospray ionization mass spectrometry). The limit of detection (50 pM) was determined for individual homologs and free polyprenols and their phosphates. Thus, it has been shown that at least some thermophilic bacteria produce not just the major C55 polyprenol as previously described, but a mixture of homologs.
PubMed: 34071687
DOI: 10.3390/microorganisms9061168 -
Polymers Dec 2023Bulgaria stands out as a country rich in diverse extreme environments, boasting a remarkable abundance of mineral hot waters, which positions it as the second-largest... (Review)
Review
Bulgaria stands out as a country rich in diverse extreme environments, boasting a remarkable abundance of mineral hot waters, which positions it as the second-largest source of such natural resources in Europe. Notably, several thermal and coastal solar salterns within its territory serve as thriving habitats for thermophilic and halophilic microorganisms, which offer promising bioactive compounds, including exopolysaccharides (EPSs). Multiple thermophilic EPS producers were isolated, along with a selection from several saltern environments, revealing an impressive taxonomic and bacterial diversity. Four isolates from three different thermophilic species, V264, 418, 423, and 438, along with the halophilic strain 28, emerged as promising candidates for further exploration. Optimization of cultivation media and conditions was conducted for each EPS producer. Additionally, investigations into the influence of aeration and stirring in laboratory bioreactors provided valuable insights into growth dynamics and polymer synthesis. The synthesized biopolymers showed excellent emulsifying properties, emulsion stability, and synergistic interaction with other hydrocolloids. Demonstrated biological activities and functional properties pave the way for potential future applications in diverse fields, with particular emphasis on cosmetics and medicine. The remarkable versatility and efficacy of biopolymers offer opportunities for innovation and development in different industrial sectors.
PubMed: 38201734
DOI: 10.3390/polym16010069 -
Frontiers in Cellular and Infection... 2023Bladder cancer (BCa) is the most common malignancy of the urinary tract which can be divided into non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder...
BACKGROUND
Bladder cancer (BCa) is the most common malignancy of the urinary tract which can be divided into non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC), and their microbial differences are not fully understood. This study was conducted by performing 2bRAD sequencing for Microbiome (2bRAD-M) on NMIBC and MIBC tissue samples to investigate the microbiota differences between NMIBC and MIBC individuals.
METHODS
A total of 22 patients with BCa, including 7 NMIBC and 15 MIBC, were recruited. Tumor tissues were surgically removed as samples and DNA was extracted. Type IIB restriction endonucleases were used to enzymatically cleave the microbial genome for each microbe's tag and map it to species-specific 2bRAD markers to enable qualitative and quantitative studies of microbes between MIBC and NMIBC tissues.
RESULTS
A total of 527 species were detected. The microbial diversity of NMIBC tissues was significantly higher than that of MIBC tissues. Microbial composition of the two tumor tissues was similar, where Ralstonia_sp000620465 was the most dominant species. 4 species (Acinetobacter_guillouiae, Anoxybacillus_A_rupiensis, Brevibacillus_agri and Staphylococcus_lugdunensis) were enriched in NMIBC, while Ralstonia_mannitolilytica, Ralstonia_pickettii, and Ralstonia_sp000620465 were overrepresented in MIBC. 252 discriminatory character taxa were also revealed by linear discriminant analysis effect sizea (LEfSe). Species importance point plots identified Ralstonia_sp000620465, Cutibacterium_acnes and Ralstonia_pickettii as the three most important species between the two groups. Meanwhile, functional annotation analysis showed 3011 different COGs and 344 related signaling pathways between MIBC and NMIBC microbiome.
CONCLUSION
This first 2bRAD-M microbiome study on MIBC and NMIBC tissues revealed significant differences in the microbial environment between the two groups, which implies a potential association between tumor microbial dysbiosis and BCa, and provides a possible target and basis for subsequent studies on the mechanisms of BCa development and progression.
Topics: Humans; Urinary Bladder; Urinary Bladder Neoplasms; Neoplasm Invasiveness
PubMed: 37351184
DOI: 10.3389/fcimb.2023.1182322 -
PloS One 2016Brevibacillus laterosporus is a spore-forming bacterium that causes a secondary infection in beehives following European Foulbrood disease. To better understand the... (Comparative Study)
Comparative Study
Brevibacillus laterosporus is a spore-forming bacterium that causes a secondary infection in beehives following European Foulbrood disease. To better understand the contributions of Brevibacillus bacteriophages to the evolution of their hosts, five novel phages (Jenst, Osiris, Powder, SecTim467, and Sundance) were isolated and characterized. When compared with the five Brevibacillus phages currently in NCBI, these phages were assigned to clusters based on whole genome and proteome synteny. Powder and Osiris, both myoviruses, were assigned to the previously described Jimmer-like cluster. SecTim467 and Jenst, both siphoviruses, formed a novel phage cluster. Sundance, a siphovirus, was assigned as a singleton phage along with the previously isolated singleton, Emery. In addition to characterizing the basic relationships between these phages, several genomic features were observed. A motif repeated throughout phages Jenst and SecTim467 was frequently upstream of genes predicted to function in DNA replication, nucleotide metabolism, and transcription, suggesting transcriptional co-regulation. In addition, paralogous gene pairs that encode a putative transcriptional regulator were identified in four Brevibacillus phages. These paralogs likely evolved to bind different DNA sequences due to variation at amino acid residues predicted to bind specific nucleotides. Finally, a putative transposable element was identified in SecTim467 and Sundance that carries genes homologous to those found in Brevibacillus chromosomes. Remnants of this transposable element were also identified in phage Jenst. These discoveries provide a greater understanding of the diversity of phages, their behavior, and their evolutionary relationships to one another and to their host. In addition, they provide a foundation with which further Brevibacillus phages can be compared.
Topics: Amino Acid Sequence; Bacteriophages; Base Sequence; Brevibacillus; DNA Replication; DNA, Viral; Gene Expression Regulation, Viral; Genetic Variation; Genome, Viral; Genomics; Microscopy, Electron, Transmission; Phylogeny; Proteomics; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Viral Proteins; Virion
PubMed: 27304881
DOI: 10.1371/journal.pone.0156838 -
3 Biotech Jun 2021Banana ( spp.), a major cash and staple fruit crop in many parts of the world, is infected by wilt, which contributes up to 100% yield loss and causes social... (Review)
Review
UNLABELLED
Banana ( spp.), a major cash and staple fruit crop in many parts of the world, is infected by wilt, which contributes up to 100% yield loss and causes social consequences. Race 1 and race 2 of Panama wilt caused by f. sp. () are prevalent worldwide and seriously affect many traditional varieties. The threat of tropical race 4 ( TR4) is looming large in African counties. However, its incidence in India has been confined to Bihar (Katihar and Purnea), Uttar Pradesh (Faizabad), Madhya Pradesh (Burhanpur) and Gujarat (Surat). Management of races by employing fungicides is often not a sustainable option as the disease spread is rapid and they negatively alter the biodiversity of beneficial ectophytes and endophytes. Besides, soil drenching with carbendazim/trifloxystrobin + tebuconazole is also not effective in suppressing the wilt of banana. Improvement of resistance to wilt in susceptible cultivars is being addressed through both conventional and advanced breeding approaches. However, engineering of banana endosphere with bacterial endophytes from resistant genotypes like Pisang lilly and YKM5 will induce the immune response against , irrespective of races. The composition of the bacterial endomicrobiome in different banana cultivars is dominated by the phyla Proteobacteria, Bacteroidetes and Actinobacteria. The major bacterial endophytic genera antagonistic to are , , , , , , , , spp., sp., spp. , , , , , , , , , , , , , , , , , , , , , , , , and . These bacterial endophytes promote the growth of banana plantlets by solubilising phosphate, producing indole acetic acid and siderophores. Application of banana endophytes during the hardening phase of tissue-cultured clones serves as a shield against . Hitherto, MAMP molecules of endophytes including flagellin, liposaccharides, peptidoglycans, elongation factor, cold shock proteins and hairpins induce microbe-associated molecular pattern (MAMP)-triggered immunity to suppress plant pathogens. The cascade of events associated with ISR and SAR is induced through MAPK and transcription factors including WRKY and MYC. Studies are underway to exploit the potential of antagonistic bacterial endophytes against isolates and to develop an understanding of the MAMP-triggered immunity and metabolomics cross talk modulating resistance. This review explores the possibility of harnessing the potential bacterial endomicrobiome against and developing nanoformulations with bacterial endophytes for increased efficacy against lethal pathogenic races of infecting banana.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13205-021-02833-5.
PubMed: 34017673
DOI: 10.1007/s13205-021-02833-5 -
Microorganisms Jul 2021The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding... (Review)
Review
The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8-70 °C and pH range 6.0-7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960-2090 m above sea level and are located on the Alpide (Alpine-Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus-Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (, , and ) have been reported, some of which may be representative of novel species (sharing 91-97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of K1, as well as of the potentially new sp. J25 and sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.
PubMed: 34361908
DOI: 10.3390/microorganisms9071473 -
Frontiers in Microbiology 2022This study focused on evaluating the influence of and strains on egg production, egg quality, immune response and antioxidant function, apparent fecal amino acid...
Enhancing egg production and quality by the supplementation of probiotic strains ( and ) improved amino acid digestibility, intestinal health, immune response, and antioxidant activity.
This study focused on evaluating the influence of and strains on egg production, egg quality, immune response and antioxidant function, apparent fecal amino acid digestibility, and jejunal morphology when supplemented as probiotics in the diets of laying hens in the peak phase. A total of 288 healthy 30-week-old Hy-Line Brown laying hens were arbitrarily assigned to four dietary groups, which included control diet and control diet supplemented with 0.02% zlc-17, lwc-13, or zlb-z1, for 84 days. The results showed that dietary and sp. exerted a positively significant influence ( ≤ 0.05) compared to the control group on the performance, egg quality, and physiological response of the birds. The diets could reduce mortality rate and enhance ( ≤ 0.05) egg weight and egg mass, egg production rate, and feed efficiency. Further analysis suggested that the probiotic strains can enhance ( ≤ 0.05) eggshell quality, Haugh unit, thick albumen content, and albumen height. Also, probiotics enhanced ( ≤ 0.05) the antioxidant status increased antioxidant enzymes and jejunal morphology as evidenced by increased villi surface area (VSA), the ratio of villi height to crypt depth, villi width, and villi height, and a significant reduction in crypt depth. Besides, nutrient absorption and retention were enhanced, as apparent fecal amino acid digestibility of key essential amino acids was substantially improved in the diet-based group. The concentrations of immunoglobulin M and A (IgM and IgA) increased significantly ( ≤ 0.05) in the probiotics group and the same effect was notable for complement proteins (C3) and immune organ (Spleen). Conclusively, the supplementation of zlc-17 in comparison to lwc-13 and zlb-z1 strains significantly ( ≤ 0.05) promoted the antioxidant status, modulated the intestinal structure, enhanced amino acid digestibility, and regulated the immunity index of the laying hens, which finally improves the laying performance and egg quality of the laying hens.
PubMed: 36177461
DOI: 10.3389/fmicb.2022.987241