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Life (Basel, Switzerland) Oct 2022Agarwood () is one of the most important resin-containing plants used to produce agar around the world and it is a precious herbal medicine usually combined with other...
Agarwood () is one of the most important resin-containing plants used to produce agar around the world and it is a precious herbal medicine usually combined with other herbs. In this study, we used the Illumina sequencing technique to explore the agarwood bacterial community structure from four different incense formations of agarwood, including healthy agarwood, drilling agarwood, liquid fermentation agarwood, and insect attack agarwood. Our results showed that 20 samples of three different incense-formation methods of agarwood and healthy agarwood acquired 1,792,706 high-quality sequences. In-depth investigation showed that when the diversity of agarwood bacterial species was higher, the agarwood incense quality was higher as well. Among healthy agarwood, drilling agarwood, fermentation agarwood, and insect attack agarwood, the bacterial community structure had significant changes. Natural agarwood, such as insect attack agarwood, kept more bacterial community structure, and the incense quality was better. Furthermore, we observed that in the healthy agarwood, and were the predominant bacteria. , , and were the dominant bacteria in the drilling agarwood. Additionally, and were some of the main bacteria in the fermentation liquid agarwood and the insect attack agarwood, while and were the dominant bacteria. This research provides a basis for further research into the underlying mechanisms of incense production, as well as the bacterial community applications of agarwood production.
PubMed: 36362852
DOI: 10.3390/life12111697 -
MBio Oct 2017We identified a crypt-specific core microbiota (CSCM) dominated by strictly aerobic, nonfermentative bacteria in murine cecal and proximal colonic (PC) crypts and...
We identified a crypt-specific core microbiota (CSCM) dominated by strictly aerobic, nonfermentative bacteria in murine cecal and proximal colonic (PC) crypts and hypothesized that, among its possible functions, it may affect epithelial regeneration. In the present work, we isolated representative CSCM strains using selective media based upon our initial 16S rRNA-based molecular identification (i.e., , , and ). Their tropism for the crypt was confirmed, and their influence on epithelial regeneration was demonstrated by monocolonization of germfree mice. We also showed that lipopolysaccharide (LPS), through its endotoxin activity, was the dominant bacterial agonist controlling proliferation. The relevant molecular mechanisms were analyzed using colonic crypt-derived organoids exposed to bacterial sonicates or highly purified LPS as agonists. We identified a Toll-like receptor 4 (TLR4)-dependent program affecting crypts at different stages of epithelial differentiation. LPS played a dual role: it repressed cell proliferation through RIPK3-mediated necroptosis of stem cells and cells of the transit-amplifying compartment and concurrently enhanced cell differentiation, particularly the goblet cell lineage. The LPS from crypt-specific core microbiota controls intestinal epithelium proliferation through necroptosis of stem cells and enhances cell differentiation, mainly the goblet cell lineage.
Topics: Animals; Apoptosis; Cell Differentiation; Cell Proliferation; Cells, Cultured; Colon; Epithelial Cells; Gastrointestinal Microbiome; Gram-Negative Bacteria; Intestinal Mucosa; Lipopolysaccharides; Mice; Stem Cells
PubMed: 29042502
DOI: 10.1128/mBio.01680-17 -
Cureus Jun 2022Background Bile inhibits bacterial growth because it is rich in bacteriostatic compounds such as bile acids. Analytical techniques using a high-intensity sequencer...
Background Bile inhibits bacterial growth because it is rich in bacteriostatic compounds such as bile acids. Analytical techniques using a high-intensity sequencer recently revealed bacterial flora in the bile of normal gallbladders in brain-dead patients. Therefore, we performed a microbial flora analysis of bile collected from pathologically normal gallbladders surgically removed from patients with hepatobiliary pancreatic diseases and normal liver function. Methods Bacterial DNA was extracted from bile samples and analyzed using 16S rRNA sequencing. Results The culture results of all 12 bile samples were negative. However, the results of the 16S ribosome gene analysis suggested the presence of bacterial flora in all samples. The phyla , , , and, more specifically, the genera , , , , , , and were detected in all 12 samples. The results of the 16S rRNA gene profile analysis revealed that and accounted for 58.62%-87.63% of the bacteria identified in each sample. Conclusion In a bacterial flora analysis targeting the 16S ribosomal gene, a specific bacterial flora was detected in bile collected from the pathologically normal gallbladders of patients with hepatobiliary pancreatic diseases. Although a diverse bacterial flora was previously reported in the bile of brain-dead patients, the present results revealed a simple bacterial flora with no diversity in the bile samples.
PubMed: 35812645
DOI: 10.7759/cureus.25681 -
Applied and Environmental Microbiology Apr 2017Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety...
Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera , , , and from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1:1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. l,d-Transpeptidase was the only significantly upregulated lytic gene in EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.
Topics: Acinetobacter; Antibiosis; Bacteria; Bacterial Physiological Phenomena; Bacterial Toxins; Cyanobacteria; Eutrophication; Fresh Water; Gene Expression Profiling; Heat-Shock Proteins; Lakes; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, RNA; Sweden; Water Microbiology
PubMed: 28115385
DOI: 10.1128/AEM.02634-16 -
Biotechnology Reports (Amsterdam,... Mar 2023Selenium nanoparticles (SeNPs) have antimicrobial and antifungal activity. SeNPs using Se resistant bacteria is a low cost and eco-friendly technology. Fungal...
Selenium nanoparticles (SeNPs) have antimicrobial and antifungal activity. SeNPs using Se resistant bacteria is a low cost and eco-friendly technology. Fungal contamination of wood during drying is one of the main causes of economic losses in the wood industry. The bacterium sp. 5 resistance to Se and its ability to produce SeNPs able to inhibit the growth of the wood brown-rotting fungus was analyzed The strain showed an optimal SeNPs production when selenite concentration was 160 mg . The SeNPs were spherical with an average size 192.33 ± 8.6 nm and a zeta potential of -41.4 ± 1.3 nm. The SeNPs produced by sp. 5 (33.6 ± 0.1 mg Se) inhibited the growth of in agar plates and in (Lenga) wood samples. sp. 5 SeNPs could be used for embedding lenga wood prior to drying for preventing the growth of the deteriorating fungi .
PubMed: 36818378
DOI: 10.1016/j.btre.2023.e00787 -
Saudi Journal of Biological Sciences Sep 2019In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of , growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and...
In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of , growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and energy source in a batch culture. ESM-1 was characterized by a polyphasic approach. The strain was identified as at similarity level of 99.9% of the 16S rRNA gene sequences. Results of the Biolog Gen III MicroPlate test system showed that strain ESM-1 reacted positively to 47 (50%) including the one-carbon compound formic acid, and partially positive to 6 (∼6.4%) out of the 94 different the traits examined. The total cellular fatty acids composition of the strain ESM-1 was (Cω7/Cω6) and C) and matched that of at a similarity index of 0.9, providing a robustness to the ESM-1 identification. Furthermore, ESM-1 displayed a complex polar lipid profile consisting of phosphatidylethanolamine, phosphatidylglycerol, glycolipid, aminolipid, in addition to uncharacterized lipids. The DNA G+C content of the strain was 66.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain ESM1-1 was clearly clustered within the clade and constructed a monophyletic subcluster with NBRC14950. The results addressed that ESM-1 is a facultative methylotrophic bacterium indigenous to Al Hofouf region and opens the door for potential biotechnological applications (e.g., bioremediation) of this strain, in future. Additionally, these findings assure that the total cellular fatty acid analysis and 16S rRNA gene are reliable tool for bacterial characterization and identification.
PubMed: 31516356
DOI: 10.1016/j.sjbs.2018.05.015 -
MSphere Aug 2022To characterize the effects of time of day for harvest on the fermentation parameters, bacterial community, and metabolic characteristics of sorghum-sudangrass hybrid...
To characterize the effects of time of day for harvest on the fermentation parameters, bacterial community, and metabolic characteristics of sorghum-sudangrass hybrid (SSG) silage, SSG (vegetative stage) harvested at 7:00 (AM), 12:00 (M), and 17:00 (PM) on three sunny days were ensiled for 1, 3, 7, 14, 30, and 60 days. Compared to AM silage, M and PM silages were characterized by delayed fermentation, unnormal lower final pH, and lower acetic acid production. In addition, PM silage contained higher residual water-soluble carbohydrates than other silages. After 60 days of ensiling, AM silage was dominated by , whereas the bacterial communities of M and PM silages were complex and mainly composed of bacteria such as , , , Acinetobacter, and . The harvest time affected a wide range of metabolic pathways including "Metabolism" and "Cellular Processes" and "Organismal Systems" in SSG silage. Particularly, at the late stage of ensiling M silage exhibited highest relative abundances of amino acid metabolisms including "glycine, serine, and threonine metabolism," "phenylalanine metabolism," and lowest relative abundances of "lysine biosynthesis." These results suggest that the time of day for harvest could affect the fermentation parameters, bacterial community, and metabolic characteristics of SSG silage. Better SSG silage characteristics could be achieved through morning harvest. Ensiling is a common way for preserving green forages worldwide. Silage fermentation quality can vary greatly depending on the chemical and microbial characteristics of forage crop being ensiled. It is well documented that forages exhibit considerable variations in chemical composition and epiphytic microbiota during daylight. However, the effects of the time of day for harvest on silage fermentation is less investigated. Our results demonstrate that the time of day for harvest could affect the fermentation parameters, bacterial community, and metabolic characteristics of SSG hybrid silage. Harvesting SSG late in the day delayed fermentation process, lowered acetic acid production and final pH, and increased the residual water-soluble carbohydrates content in silage. Moreover, the delayed harvest time increased the relative abundances of bacteria such as , , Acinetobacter, , and , and amino acid metabolisms at the late stage of SSG ensiling. This study highlights the importance of diurnal changes in forage to fermentation characteristics, providing a strategy to improve silage quality through optimizing the harvest time.
Topics: Amino Acids; Bacteria; Carbohydrates; Fermentation; Silage; Sorghum; Water
PubMed: 35862805
DOI: 10.1128/msphere.00168-22 -
PloS One 2016The gut microbiota has a crucial role in the growth, development and environmental adaptation in the host insect. The objective of our work was to investigate the...
The gut microbiota has a crucial role in the growth, development and environmental adaptation in the host insect. The objective of our work was to investigate the microbiota of the healthy silkworm Bombyx mori gut and changes after the infection of B. mori cypovirus (BmCPV). Intestinal contents of the infected and healthy larvae of B. mori of fifth instar were collected at 24, 72 and 144 h post infection with BmCPV. The gut bacteria were analyzed by pyrosequencing of the 16S rRNA gene. 147(135) and 113(103) genera were found in the gut content of the healthy control female (male) larvae and BmCPV-infected female (male) larvae, respectively. In general, the microbial communities in the gut content of healthy larvae were dominated by Enterococcus, Delftia, Pelomonas, Ralstonia and Staphylococcus, however the abundance change of each genus was depended on the developmental stage and gender. Microbial diversity reached minimum at 144 h of fifth instar larvae. The abundance of Enterococcus in the females was substantially lower and the abundance of Delftia, Aurantimonas and Staphylococcus was substantially higher compared to the males. Bacterial diversity in the intestinal contents decreased after post infection with BmCPV, whereas the abundance of both Enterococcus and Staphylococcus which belongs to Gram-positive were increased. Therefore, our findings suggested that observed changes in relative abundance was related to the immune response of silkworm to BmCPV infection. Relevance analysis of plenty of the predominant genera showed the abundance of the Enterococcus genus was in negative correlation with the abundance of the most predominant genera. These results provided insight into the relationship between the gut microbiota and development of the BmCPV-infected silkworm.
Topics: Animal Husbandry; Animals; Bombyx; Female; Gastrointestinal Microbiome; Host-Pathogen Interactions; Larva; Male; Reoviridae
PubMed: 26745627
DOI: 10.1371/journal.pone.0146313 -
BioMed Research International 2016Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. MTQ3 is a member of PGPR that produces siderophores. The...
Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. MTQ3 is a member of PGPR that produces siderophores. The draft genome sequence of MTQ3 has been reported. Here, we analyzed the genome sequence of MTQ3 and performed a comparative genome analysis of four sequenced strains, revealing genetic relationships among these strains. In addition, genes responsible for bacteriocin and nonribosomal peptide synthesis were detected in the genomes of each strain. To reveal the functions of NRPS genes in siderophore production in MTQ3, three NRPS genes were knocked out to obtain the three mutants MTQ3-Δ1941, MTQ3-Δ1945, and MTQ3-Δ1946, which were compared with the wild-type strain. In qualitative and quantitative analyses using CAS assay, the mutants failed to produce siderophores. Accordingly, the NRPS genes in MTQ3 were functionally related to siderophore production. These results clarify one mechanism by which plant growth is promoted in MTQ3 and have important applications in agricultural production.
Topics: Delftia; Gene Knockout Techniques; Genome, Bacterial; Peptides; Phylogeny; Siderophores
PubMed: 27847812
DOI: 10.1155/2016/3687619 -
Frontiers in Microbiology 2019To counteract bacterial defense systems, bacteriophages (phages) make extensive base modifications (substitutions) to block endonuclease restriction. Here we evaluated...
To counteract bacterial defense systems, bacteriophages (phages) make extensive base modifications (substitutions) to block endonuclease restriction. Here we evaluated Type II restriction of three thymidine (T or 5-methyldeoxyuridine, 5mdU) modified phage genomes: phage M6 with 5-(2-aminoethyl)deoxyuridine (5-edU), phage ViI (Vi1) with 5-(2-aminoethoxy)methyldeoxyuridine (5-emdU) and phage phi W-14 (a.k.a. ΦW-14) with α-putrescinylthymidine (putT). Among >200 commercially available restriction endonucleases (REases) tested, phage M6, ViI, and phi W-14 genomic DNAs (gDNA) show resistance against 48.4, 71.0, and 68.8% of Type II restrictions, respectively. Inspection of the resistant sites indicates the presence of conserved dinucleotide TG or TC (TS, S=C, or G), implicating the specificity of TS sequence as the target that is converted to modified base in the genomes. We also tested a number of DNA methyltransferases (MTases) on these phage DNAs and found some MTases can fully or partially modify the DNA to confer more resistance to cleavage by REases. Phage M6 restriction fragments can be efficiently ligated by T4 DNA ligase. Phi W-14 restriction fragments show apparent reduced rate in exonuclease III degradation. This work extends previous studies that hypermodified T derived from 5hmdU provides additional resistance to host-encoded restrictions, in parallel to modified cytosines, guanine, and adenine in phage genomes. The results reported here provide a general guidance to use REases to map and clone phage DNA with hypermodified thymidine.
PubMed: 30984133
DOI: 10.3389/fmicb.2019.00584