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131条结果
  • 机译 大肠杆菌中产甲烷嗜热杆菌自养营养菌RFAP合酶的纯化,动力学表征和定点诱变
    摘要:Methane-producing archaea are among a select group of microorganisms that utilize tetrahydromethanopterin (H4MPT) as a one-carbon carrier instead of tetrahydrofolate. In H4MPT biosynthesis, β-ribofuranosylaminobenzene 5′-phosphate (RFAP) synthase catalyzes the production of RFAP, CO2, and pyrophosphate from p-aminobenzoic acid (pABA) and phosphoribosyl-pyrophosphate (PRPP). In this work, to gain insight into amino acid residues required for substrate binding, RFAP synthase from Methanothermobacter thermautotrophicus was produced in Escherichia coli, and site-directed mutagenesis was used to alter arginine 26 (R26) and aspartic acid 19 (D19), located in a conserved sequence of amino acids resembling the pABA binding site of dihydropteroate synthase. Replacement of R26 with lysine increased the KM for pABA by an order of magnitude relative to wild-type enzyme without substantially altering the KM for PRPP. Although replacement of D19 with alanine produced inactive enzyme, asparagine substitution allowed retention of some activity, and the KM for pABA increased about threefold relative to wild-type enzyme. A molecular model developed by threading RFAP synthase onto the crystal structure of homoserine kinase places R26 in the proposed active site. In the static model, D19 is located close to the active site, yet appears too far away to influence ligand binding directly. This may be indicative of the protein conformational change predicted previously in the Bi-Ter kinetic mechanism and/or formation of the active site at the interface of two subunits. Due to the vital role of RFAP synthase in H4MPT biosynthesis, insights into the mode of substrate binding and mechanism could be beneficial for developing RFAP synthase inhibitors designed to reduce the production of methane as a greenhouse gas.
  • 机译 15种临床志贺氏菌的比较基因组分析弗氏杆菌菌株的毒力和抗生素耐药性
    摘要:Shigellosis is the major cause of dysentery globally. It is mainly attributed to two Shigella species, Shigella sonnei and Shigella flexneri, which leads to approximately 165 million infections and 1.1 million deaths each year. Rapid increase and widening of spectrum in antibiotics resistance make Shigella hard to be adequately controlled through existing prevention and treatment measures. It has also been observed that enhanced virulence and advent of antibiotic resistance (AR) could arise almost simultaneously. However, genetic linkages between the two factors are missing or largely ignored, which hinders experimental verification of the relationship. In this study, we sequenced 15 clinically isolated S. flexneri strains. Genome assembly, annotation and comparison were performed through routine pipelines. Differential resistant profiles of all 15 S. flexneri strains to nine antibiotics were experimentally verified. Virulence factors (VFs) belonging to 4 categories and 31 functional groups from the Virulence Factor Database (VFDB) were used to screen all Shigella translated CDSs. Distribution patterns of virulence factors were analysed by correlating with the profiles of bacterial antibiotics resistance. In addition, multi-resistant S. flexneri strains were compared with antibiotic-sensitive strains by focusing on the abundance or scarcity of specific groups of VFs. By doing these, a clear view of the relationships between virulence factors and antibiotics resistance in Shigella could be achieved, which not only provides a set of genetic evidence to support the interactions between VFs and AR but could also be used as a guidance for further verification of the relationships through manipulating specific groups of virulence factors.
  • 机译 军团菌的分离与鉴定。伊朗西南部基于巨噬细胞感染性增强子(mip)基因测序的环境水污染
    摘要:Legionella species are widespread in natural water sources and man-made aqueous environments, as well as fresh-water. The present study was conducted owing to the lack of research regarding the prevalence of Legionella spp in the water sources of Ahvaz city in southwest Iran. In this study the macrophage infectivity potentiator (mip) gene sequencing was used for identification of various Legionella species isolated from different water sources. In this study, 144 water samples were collected and inoculated on the buffered charcoal-yeast extract (BCYE) agar and modified Wadowsky-Yee (MWY) medium. The DNA was extracted from positive cultures. The Legionella species were confirmed by amplifying a 654 bp fragment of the 16S rRNA gene. The mip gene of all isolates were amplified by PCR and purified for sequencing. The mip gene sequences were analyzed by jPHYDIT software version 1. The results showed a 13.9% (20/144) prevalence of Legionella spp. in water sources of Ahvaz city, southwest Iran. Analyzing of the mip gene sequences showed, out of 20 Legionella isolates, 13 isolates (54.1%) were positive for L. pneumophila, 5 isolates (20.8%) were positive for L. worsleinsis, one isolates for each one of L. dumoffi and L. fairfieldensis, (4.1%). According to our research, the occurrence of Legionella spp in water sources could be a hazard for the health systems especially in the hospitals. The regular monitoring of these water sources by health planners may therefore be useful for decreasing the risk for Legionella spp. infections.
  • 机译 绵羊,山羊和骆驼生肉中的鲍曼不动杆菌:毒力和抗生素抗性模式
    摘要:Acinetobacter genus belongs to a group of Gram-negative coccobacillus. These bacteria are isolated from human and animal origins. Antimicrobial agents play a vital role in treating infectious diseases in both humans and animals, and Acinetobacter in this regard is defined as an organism of low virulence. The current study aimed to evaluate antibiotic resistance properties and virulence factor genes in Acinetobacter baumannii strains isolated from raw animal meat samples. Fresh meat samples from 124 sheep, 162 goat, and 95 camels were randomly collected from Isfahan and Shahrekord cities in Iran. Most A. baumannii strains isolated from sheep meat samples represented fimH (82.35%), aac(3)-IV (78.43%), sul1 (78.43%) and Integron Class I (96.07%) genes. Moreover, more than 50% of A. baumannii strains isolated from sheep samples were resistant to streptomycin (54.90%), gentamycin (74.50%), co-trimoxazole (70.58%), tetracycline (82.35%), and trimethoprim (62.74%). Current findings revealed significant association between the presence of fimH, cnfI, afa/draBC, dfrA1, sulI, aac(3)-IV genes in sheep samples. Furthermore, significant association was observed between fimH, cnfI, sfa/focDE and dfrA1genes in goat meat samples. In sheep meat samples, significant differences were identified in resistance to gentamicin, tetracycline, and co-trimoxazole in comparison with other antibiotics. Finally, there were statistically significant differences between the incidences of resistance to gentamicin, tetracycline, and co-trimoxazole in comparison with other antibiotics in all strains. In conclusion, the presence of virulence factors and antibiotic resistance in A. baumannii strains isolated from animal meat samples showed that animals should be considered as a potential reservoir of multidrug-resistant A. baumannii.
  • 机译 金黄色葡萄球菌噬菌体vB_SauS_SA2的分离与鉴定
    摘要:A novel bacteriophage vB_SauS_SA2 (hereafter designated SA2) that infects Staphylococcus aureus was isolated. At a multiplicity of infection (MOI) of 0.1, phage SA2 had a latent period of about 10 min with a burst size of 293 PFUs/infected cell (PFU, plaque forming unit). Phage SA2 had a double-stranded DNA genome with a length of 89,055 bp and a G + C content of 31.9%. The genome contained 130 open reading frames (ORFs), 28 of which had assigned functions, and 18 were unique. One tRNA gene (tRNAAsn) was discovered, and no virulence genes were identified. Its genome showed very low similarity with phage genomes deposited in public databases (75% nucleotide identity and 7% query coverage). The unique characteristics of phage SA2 led to the proposal of a new Siphoviridae genus named ‘SA2likevirus’.
  • 机译 重组蛋白在生物膜中的表达
    摘要:Biofilm research is usually focused on the prevention or control of biofilm formation. Recently, the significance of the biofilm mode of growth in biotechnological applications received increased attention. Since biofilm reactors show many advantages over suspended cell reactors, especially in their higher biomass density and operational stability, bacterial biofilms have emerged as an interesting approach for the expression of specific proteins. Despite the potential of biofilm systems, recombinant protein production using biofilms has been scarcely investigated for the past 25 years. Our group has demonstrated that E. coli biofilms were able to produce a model recombinant protein, the enhanced green fluorescent protein (eGFP), at much higher levels than their planktonic counterparts. Even without optimization of cultivation conditions, an attractive productivity was obtained, indicating that biofilm cultures can be used as an alternative form of high cell density cultivation (HCDC). E. coli remains one of the favorite hosts for recombinant protein production and it has been successfully used in metabolic engineering for the synthesis of high value products. This review presents the advantages and concerns of using biofilms for the production of recombinant proteins and summarizes the different biofilm systems which have been described for this purpose. The relative advantages and disadvantages of the four microbial hosts tested for recombinant protein production in biofilms (two bacteria and two filamentous fungi) are also discussed.
  • 机译 地中海中的微生物酶:与气候变化的关系
    摘要:In most of the aquatic ecosystems, microorganisms are major players in the biogeochemical and nutrients cycles (Carbon Nitrogen, Phosphorus), through their enzymatic activities (leucine aminopeptidase, alkaline phosphatase and beta-glucosidase) on organic polymers such as polypeptides, organophosphate esters and polysaccharides, respectively. The small monomers released by decomposition are metabolised by microbes, supporting their growth. Most of the extracellular enzymes are adaptative and their synthesis and activity is strongly affected by environmental factors, consequently the relative importance of leucine aminopeptidase, alkaline phosphatase and beta-glucosidase reflects differences in the composition of organic matter and assume a different meaning.Since more than two decades, at the CNR the influence of climate changes, seasonal variability, depth and coastal input on the patterns of enzymatic activities in the Mediterranean Sea have been studied. Its particular characteristics of a semi-closed basin, high summer evaporation and the occurrence of important water dynamics, make this ecosystem particularly suitable as a model site for climate changes-related observations.The present paper reviews the current information of environmental changes on extracellular enzymatic activity obtained in the Mediterranean areas with the aim of evaluating the effects of environmental changes on the microbial activities. The obtained results revealed significant variations in the rates of hydrolytic activities in relation to space and time, with the highest levels generally found in the epipelagic layer (0–100m) and in coastal zones during warm periods. In the Central Mediterranean Sea their relationship with temperature changes was demonstrated.Spatial variations in the relative enzyme activities also suggested a modulation in the metabolic profiles of the prokaryotic communities, with biogeochemical implications in nutrient regeneration.Long term studies on microbial activity and abundances in relation with rising temperatures can have a predictive value to describe the evolutionary scenario of microbial processes and the response of microbial metabolism to climate changes in the Mediterranean Sea.
  • 机译 耐甲氧西林金黄色葡萄球菌(MRSA)和某些药用植物提取物的抗MRSA活性:简要综述
    摘要:The increasing emergence of multidrug-resistant infection causing microorganisms has become a significant burden globally. Despite the efforts of pharmaceuticals in producing relatively new antimicrobial drugs, they have resulted in a high rate of mortality, disability and diseases across the world especially in developing countries. Supporting this claim was the report of the Centre for Disease Control and Prevention (CDC) who estimated that over 2 million illnesses and 23,000 deaths per year are attributable to antibiotic resistant pathogens in the United States. They include Methicillin-resistant Staphylococcus aureus (MRSA), Vancomycin-intermediate Staphylococcus aureus (VISA), Vancomycin-resistant Staphylococcus aureus (VRSA), Vancomycin-resistant enterococci (VRE), Extended spectrum beta-lactamases (ESBLs) producing gram-negative bacilli, Multidrug-resistant Streptococcus pneumoniae (MDRSP), Carbapenem-resistant Enterobacteriaceae (CRE) and Multidrug-resistant Acinetobacter baumannii. For MRSA, resistance is as a result of Methicillin-sensitive S. aureus (MSSA) strains that have acquired Staphylococcal Cassette Chromosome mec (SCCmec) which carries mecA gene. The gene encodes the penicillin-binding protein (PBP2a) which confers resistance to all β-lactam antibiotics. Vancomycin was previously the widely preferred drug for the treatment of MRSA infections. It is no longer the case with the emergence of S. aureus strains with reduced vancomycin sensitivity limiting the conventional treatment options for MRSA infections to very scanty expensive drugs. Presently, many researchers have reported the antibacterial activity of many plant extracts on MRSA. Hence, these medicinal plants might be promising candidates for treatment of MRSA infections. This work is a brief review on Methicillin-resistant Staphylococcus aureus (MRSA) and the anti-MRSA activities of extracts of selected medicinal plants.
  • 机译 腐殖质病原体持续存在的条件下的细胞亚型
    摘要:The paper discusses the issues of morphofunctional variability of causative agents of sapronoses under stressful environmental conditions. In the current century, sapronoses infections attract more and more attention. Under unfavorable habitat conditions, their pathogens use a strategy for the formation of resting (stable) states: viable but non-cultured cell forms and the persistence of bacteria, which are characterized by reduced metabolism, changes in the morphology and physiology of microorganisms, and termination of their replication. With the formation of resistant forms of bacteria, the possibility of survival of sapronoses causative agents in the interepidemic period, the formation of their antibiotic resistance, which plays an important role in the chronicity of infections, is associated. The literature widely discusses the mechanisms and conditions for the formation of resistant states of pathogenic bacteria, their pathogenetic significance in infectious pathology, whereas the ultrastructural organization and morphological variability of resistant cellular forms, as well as their differentiation, causing the heterogeneity of the pathogens population, are not yet well covered. The emergence of molecular cell biology methods and the discovery of genetic modules of toxin-antitoxin systems revealed a single mechanism for regulating the formation of resistant cellular forms of bacteria. This served as the basis for the development of fundamentally new technologies for the study of the mechanisms for the conservation of the pathogenic potential of resistant cellular forms of pathogens of natural focal sapronosis in interepidemic periods. Based on the analysis of current data, as well as their own experience, the authors assess the role of morphofunctional changes in resistant cellular forms of bacteria and their significance in the adaptation strategies of causative agents of sapronoses (on the example of Yersinia pseudotuberculosis). The study of the manifestations of heteromorphism of causative agents of sapronoses forms the paradigm of the need to improve methods for detecting resistant forms of these bacteria in human and animal biomaterial in order to diagnose chronic recurrent and persistent infections, create effective strategies for monitoring and monitoring the environment.
  • 机译 直接从临床样本中检测金黄色葡萄球菌,潘顿-华伦特白花青素和耐甲氧西林的实时荧光定量PCR检测
    摘要:Rapid detection of Methicillin Resistant Staphylococcus aureus (MRSA) is an important concern for both treatment and implementation of infection control policies. The present study provides an ‘in house’ real-time PCR assay to detect directly nuc, pvl, and mecA genes. The assay is able to perform identification of MRSA, Methicillin-Sensitive S. aureus, Methicillin-Resistant Coagulase Negative Staphylococci and the Panton-Valentine leukocidin virulence gene from rectal and pharyngeal swab samples in a screening context. We found an analytical sensitivity of this current Triplex PCR assay of 514 CFU/mL. Analytical specificity was tested with different Gram-positive and Gram-negative species and yielded no false-positive PCR signal. The sensitivity and specificity of the Triplex Real Time PCR were both 100% for these targets when compared with the culture and conventional methods. This assay is readily adaptable for routine use in a microbiology laboratory, as it will enable the implementation of timely and properly guided therapy and infection control strategies.
  • 机译 噬菌体衍生的三重融合蛋白对金黄色葡萄球菌的抗菌活性
    摘要:The increasing spread of antibiotic-resistant microorganisms has led to the necessity of developing alternative antimicrobial treatments. The use of peptidoglycan hydrolases is a promising approach to combat bacterial infections. In our study, we constructed a 2 kb-triple-acting fusion gene (TF) encoding the N-terminal amidase-5 domain of streptococcal LambdaSA2 prophage endolysin (D-glutamine-L-lysin endopeptidase), a mid-protein amidase-2 domain derived from the staphylococcal phage 2638A endolysin (N-acetylmuramoyl-L-alanine amidase) and the mature version (246 residues) of the Staphylococcus simulans Lysostaphin bacteriocin (glycyl-glycine endopeptidase) at the C-terminus. The TF gene was expressed in Nicotiana benthamiana plants using the non-replicating Cowpea mosaic virus (CPMV)-based vector pEAQ-HT and the replicating Alternanthera mosaic virus (AltMV)-based pGD5TGB1L8823-MCS-CP3 vector, and in Escherichia coli using pET expression vectors pET26b+ and pET28a+. The resulting poor expression of this fusion protein in plants prompted the construction of a TF gene codon-optimized for expression in tobacco plants, resulting in an improved codon adaptation index (CAI) from 0.79 (TF gene) to 0.93 (TFnt gene). Incorporation of the TFnt gene into the pEAQ-HT vector, followed by transient expression in N. benthamiana, led to accumulation of TFnt to an approximate level of 0.12 mg/g of fresh leaf weight. Antimicrobial activity of purified plant- and bacterial-produced TFnt proteins was assessed against two strains of Gram-positive Staphylococcus aureus 305 and Newman. The results showed that plant-produced TFnt protein was preferentially active against S. aureus 305, showing 14% of growth inhibition, while the bacterial-produced TFnt revealed significant antimicrobial activity against both strains, showing 68 (IC50 25 µg/ml) and 60% (IC50 71 µg/ml) growth inhibition against S. aureus 305 and Newman, respectively. Although the combination of codon optimization and transient expression using the non-replicating pEAQ-HT expression vector facilitated production of the TFnt protein in plants, the most functionally active antimicrobial protein was obtained using the prokaryotic expression system.
  • 机译 巨球菌rodZ缺失突变体对钙离子的敏感性导致原生质球大小增加
    摘要:RodZ is a cytoskeletal protein associated with bacterial cell shape. It is a transmembrane protein located on the plasma membrane, and it binds to another cytoskeletal protein MreB. Deinococcus grandis contains a rodZ homolog. Although D. grandis is rod-shaped, it becomes spherical in shape when the rodZ homolog is disrupted. The rodZ deletion mutant was treated with lysozyme to generate spheroplasts. The spheroplasts enlarged in medium containing calcium chloride and penicillin. The rodZ deletion mutant spheroplasts were more sensitive to calcium ions than wild type. Cell and cytoplasm sizes of enlarged spheroplasts of the rodZ deletion mutant tended to be larger than those of wild type. Thus, disruption of rodZ enhances plasma and outer membrane expansion in D. grandis spheroplasts.
  • 机译 在多中心回顾性研究中,复发性艰难梭菌感染患者的菌群异常和VRE非殖民化的微生物组预测因子
    摘要:The gastrointestinal microbiome is intrinsically linked to the spread of antibiotic resistance. Antibiotic treatment puts patients at risk for colonization by opportunistic pathogens like vancomycin resistant Enterococcus and Clostridioides difficile by destroying the colonization resistance provided by the commensal microbiota. Once colonized, the host is at a much higher risk for infection by that pathogen. Furthermore, we know that microbiome community differences are associated with disease states, but we do not have a good understanding of how we can use these changes to classify different patient populations. To that end, we have performed a multicenter retrospective analysis on patients who received fecal microbiota transplants to treat recurrent Clostridioides difficile infection. We performed 16S rRNA gene sequencing on fecal samples collected as part of this study and used these data to develop a microbiome disruption index. Our microbiome disruption index is a simple index that is predictive across cohorts, indications, and batch effects. We are able to classify pre-fecal transplant vs post-fecal transplant samples in patients with recurrent C. difficile infection, and we are able to predict, using previously-published data from a cohort of patients receiving hematopoietic stem cell transplants, which patients would go on to develop bloodstream infections. Finally, we also identified patients in this cohort that were initially colonized with vancomycin resistant Enterococcus and that 92% (11/12) were decolonized after the transplant, but the microbiome disruption index was unable to predict such decolonization. We, however, were able to compare the relative abundance of different taxa between the two groups, and we found that increased abundance of Enterobacteriaceae predicts whether patients were colonized with vancomycin resistant Enterococcus. This work is an early step towards a better understanding of how microbiome predictors can be used to help improve patient care and patient outcomes.
  • 机译 使用响应面法优化已鉴定灵芝灵芝QRS 5120菌丝体的生物量,胞外多糖和细胞内多糖的生产
    摘要:Wild-cultivated medicinal mushroom Ganoderma lucidum was morphologically identified and sequenced using phylogenetic software. In submerged-liquid fermentation (SLF), biomass, exopolysaccharide (EPS) and intracellular polysaccharide (IPS) production of the identified G. lucidum was optimised based on initial pH, starting glucose concentration and agitation rate parameters using response surface methodology (RSM). Molecularly, the G. lucidum strain QRS 5120 generated 637 base pairs, which was commensurate with related Ganoderma species. In RSM, by applying central composite design (CCD), a polynomial model was fitted to the experimental data and was found to be significant in all parameters investigated. The strongest effect (p < 0.0001) was observed for initial pH for biomass, EPS and IPS production, while agitation showed a significant value (p < 0.005) for biomass. By applying the optimized conditions, the model was validated and generated 5.12 g/L of biomass (initial pH 4.01, 32.09 g/L of glucose and 102 rpm), 2.49 g/L EPS (initial pH 4, 24.25 g/L of glucose and 110 rpm) and 1.52 g/L of IPS (and initial pH 4, 40.43 g/L of glucose, 103 rpm) in 500 mL shake flask fermentation. The optimized parameters can be upscaled for efficient biomass, EPS and IPS production using G. lucidum.
  • 机译 EvaGreen在流式细胞仪评估单核细胞增生性李斯特菌АТСС13932细胞活力中的应用
    摘要:Determination of eukaryotic cell viability using flow cytometry is widespread and based on the use of fluorescent dyes such as SYTO, DAPI, SYBR, PI, and SYTOX. For many years, traditional microbiological methods have been used to successfully analyze prokaryotic cells, but the application of flow cytometry should be considered because it provides an opportunity for quantitative assessment. A combination of SYTO 9 or SYBR green and PI has been used successfully. DNA-binding dyes such as SYTO 9, SYBR green, and EvaGreen are used in qPCR. The aim of this study was to assess the feasibility of EvaGreen to determine the viability of Listeria monocytogenes АТСС 13932 cells using flow cytometry. RNA from Escherichia coli ATCC 25922 was isolated using the MagNA Pure LC RNA Isolation Kit-High Performance (Roche, Germany) according to the kit instructions on MagNA Pure LC® 2.0 (Roche, Switzerland). Chicken DNA was isolated using the Sorb-GMO-B kit (Syntol CJSC, Russia) according to the kit instructions. RNA from E. coli ATCC 25922, chicken DNA, a positive control, and a negative control of L. monocytogenes АТСС 13932 were stained with EvaGreen and analyzed on the Guava EasyCyte flow cytometer (Merck Millipore, Germany). Chicken DNA demonstrated both green and red fluorescence, while E. coli RNA displayed only red fluorescence. While the positive L. monocytogenes АТСС 13932 control and chicken DNA demonstrated similar fluorescence properties, the negative control showed a localization similar to that observed with E. coli RNA. Degraded ssDNA and RNA stained with EvaGreen demonstrated red fluorescence. Although EvaGreen is a class III dye, we observed fluorescence of live L. monocytogenes АТСС 13932 cells in the positive control stained with EvaGreen. The observed phenomenon was linked to the solution composition. It is necessary to repeat this analysis with various solution compositions as well as a wide range of both Gram-positive and Gram-negative bacteria to determine the effects on cell envelope permeability of EvaGreen.
  • 机译 不同测序方法反映了温带珊瑚Astrangia poculata微生物组的稳定性
    摘要:The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral's bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. To assess the impact of methodology on the detectable diversity of the coral's microbiome, we obtained near full-length Sanger sequences from clone libraries constructed from a subset of the same A. poculata samples. Eight samples were analyzed: two sets of paired symbiotic (brown) and aposymbiotic (white) colonies collected in the fall (September) and two sets collected in the spring (April). Analysis of the Sanger sequences revealed that the microbiome of A. poculata exhibited a high level of richness; 806 OTUs were identified among 1390 bacterial sequences. While the Illumina study revealed that A. poculata's microbial communities did not significantly vary according to symbiotic state, but did vary by season, Sanger sequencing did not expose seasonal or symbiotic differences in the microbiomes. Proteobacteria dominated the microbiome, forming the majority (55% to 80%) of classifiable bacteria in every sample, and the five bacterial classes with the highest mean relative portion (5% to 35%) were the same as those determined by prior Illumina sequencing. Sanger sequencing also captured the same core taxa previously identified by next-generation sequencing. Alignment of all sequences and construction of a phylogenetic tree revealed that both sequencing methods provided similar portrayals of the phylogenetic diversity within A. poculata's bacterial associates. Consistent with previous findings, the results demonstrated that the Astrangia microbiome is stable notwithstanding the choice of sequencing method and the far fewer sequences generated by clone libraries (46 to 326 sequences per sample) compared to next-generation sequencing (3634 to 48481 sequences per sample). Moreover, the near-full length 16S rRNA sequences produced by this study are presented as a resource for the community studying this model system since they provide necessary information for designing primers and probes to further our understanding of this coral's microbiome.
  • 机译 使用高通量扩增子测序和单叠氮化乙锭染料追踪接受异黄酮治疗的雌马酚生产的更年期妇女的微生物群变化
    摘要:This work describes the impact of long term consumption of an isoflavone-rich dietary daily supplement on the composition and diversity of the faecal microbiota of a menopausal, equol-producing woman. Sequencing of 16S rDNA amplicons was performed on faecal samples taken at 0, 1, 3 and 6 months of treatment. Additionally, and for comparative purposes, ethidium monoazide (EMA) was used to avoid detection of DNA from dead bacteria. Members of two genera of the family Coriobacteriaceae (Eggerthella and Collinsella) were found in greater proportions at all sampling points during isoflavone supplementation. Different genera of the family Ruminococcaceae (e.g., Ruminococcus and Faecalibacterium), as well as members of the family Lachnospiraceae (Coprococcus) also underwent significant increases. For this last genus a positive correlation with the levels of equol excretion in urine was found. Currently bacterial strains known to be involved in isoflavone metabolism and equol production have been assigned to these taxa. The use of EMA dye allowed us to unravel those bacterial gut linages (e.g., Lachnospiraceae) that were more susceptible to damage. Our study contributes to the identification of microorganisms possibly involved in the production of isoflavone-desirable metabolites (such as equol), which could ultimately be isolated and further used as probiotics by people who cannot naturally benefit from isoflavones.
  • 机译 Asgard古细菌:一系列微生物群落中的多样性,功能和进化意义
    摘要:Elucidating the diversity of the Archaea has many important ecological and evolutionary implications. The Asgard superphylum of the archaea, described recently from metagenomic data, has reignited the decades-old debate surrounding the topology of the tree of life. This review synthesizes recent findings through publicly available genomes and literature to describe the current ecological and evolutionary significance of the Asgard superphylum. Asgard archaea have been found in a diverse range of microbiomes across the globe, primarily from sedimentary environments. Within these environments, positive correlations between specific members of the Asgard archaea and Candidate Division TA06 bacteria have been observed, opening up the possibility of symbiotic interactions between the groupings. Asgard archaeal genomes encode functionally diverse metabolic pathways, including the Wood-Ljungdahl pathway as a carbon-fixation strategy, putative nucleotide salvaging pathways, and novel mechanisms of phototrophy including new rhodopsins. Asgard archaea also appear to be active in nitrogen cycling. Asgard archaea encode genes involved in both dissimilatory nitrate reduction and denitrification, and for the potential to use atmospheric nitrogen or nitrite as nitrogen sources. Asgard archaea also may be involved in the transformation of sulfur compounds, indicating a putative role in sulfur cycling. To date, all Asgard archaeal genomes identified were described as obligately anaerobic. The Asgard archaea also appear to have important evolutionary implications. The presence of eukaryotic signature proteins and the affiliation of Asgard archaea in phylogenetic analyses appears to support two-domain topologies of the tree of life with eukaryotes emerging from within the domain of archaea, as opposed to the eukaryotes being a separate domain of life. Thus far, Heimdallarchaeota appears as the closest archaeal relative of eukaryotes.
  • 机译 营养不良微生物群落的概况
    • 作者:Paola Brun
    • 刊名:AIMS Microbiology
    • 2019年第1期
    摘要:Alterations in the human gut microbiota play an important role in disease pathogenesis. Although next-generation sequencing has provided observational evidence linking shifts in gut microbiota composition to alterations in the human host, underlying mechanisms remain elusive. Metabolites generated within complex microbial communities and at the crossroads with host cells may be able to explain the impact of the gut microbiome on human homeostasis. Emerging technologies including novel culturing protocols, microfluidic systems, engineered organoids, and single-cell imaging approaches are providing new perspectives from which the gut microbiome can be studied paving the way to new diagnostic markers and personalized therapeutic interventions.
  • 机译 细胞内/表面月光蛋白,有助于肠道菌群与宿主的附着
    摘要:The gut microbiota use proteins on their surface to form and maintain interactions with host cells and tissues. In recent years, many of these cell surface proteins have been found to be identical to intracellular enzymes and chaperones. When displayed on the cell surface these moonlighting proteins help the microbe attach to the host by interacting with receptors on the surface of host cells, components of the extracellular matrix, and mucin in the mucosal lining of the digestive tract. Binding of these proteins to the soluble host protein plasminogen promotes the conversion of plasminogen to an active protease, plasmin, which activates other host proteins that aid in infection and virulence. In this mini-review, we discuss intracellular/surface moonlighting proteins of pathogenic and probiotic bacteria and eukaryotic gut microbiota.

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