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1.
Methods Mol Biol ; 2833: 35-42, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949698

RESUMO

Antimicrobial resistance (AMR) poses a serious threat to global health, potentially causing 10 million deaths per year globally by 2050. To tackle AMR, researchers from all around the world have generated a selection of various formulated (viz. nanoparticulate, liposomal) therapeutic combinations to be evaluated for new antimicrobial drug discovery. To meet the urgent need for accelerating new antibacterial drug development, we need rapid but reliable whole-cell assay methods and models to test formulated therapeutic combinations against several pathogens in different in vitro conditions as models of actual infections.Over the past two decades, high-throughput spot-culture growth inhibition assay (HT-SPOTi) has been demonstrated to be a gold-standard drug susceptibility method for evaluating novel chemotherapeutic entities and existing drugs against various microbes of global concern. Our modified HT-SPOTi method serves the purpose of evaluating drug combinations against Gram-positive/negative microorganisms as well as acid-fast bacilli. The newly developed and modified HT-SPOTi assay builds upon the limitations of our previously published method to incorporate antimicrobial susceptibility testing with formulated therapeutic combinations. The modified HT-SPOTi is compared with a range of other antimicrobial susceptibility testing methods and validated using a library of existing antibiotics as well as formulated therapeutic combinations. The modified HT-SPOTi assay can serve as an efficient and reliable high-throughput drug screening platform to discover new potential antimicrobial molecules, including as part of therapeutic formulations.This chapter describes the generation of drug susceptibility profile for formulated therapeutic combinations using modified HT-SPOTi in a semi-automated system.


Assuntos
Antibacterianos , Testes de Sensibilidade Microbiana , Testes de Sensibilidade Microbiana/métodos , Antibacterianos/farmacologia , Ensaios de Triagem em Larga Escala/métodos , Humanos , Bactérias/efeitos dos fármacos , Bactérias/crescimento & desenvolvimento
2.
Methods Mol Biol ; 2833: 93-108, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949704

RESUMO

To model complex systems, individual-based models (IBMs), sometimes called "agent-based models" (ABMs), describe a simplification of the system through an adequate representation of the elements. IBMs simulate the actions and interaction of discrete individuals/agents within a system in order to discover the pattern of behavior that comes from these interactions. Examples of individuals/agents in biological systems are individual immune cells and bacteria that act independently with their own unique attributes defined by behavioral rules. In IBMs, each of these agents resides in a spatial environment and interactions are guided by predefined rules. These rules are often simple and can be easily implemented. It is expected that following the interaction guided by these rules we will have a better understanding of agent-agent interaction as well as agent-environment interaction. Stochasticity described by probability distributions must be accounted for. Events that seldom occur such as the accumulation of rare mutations can be easily modeled.Thus, IBMs are able to track the behavior of each individual/agent within the model while also obtaining information on the results of their collective behaviors. The influence of impact of one agent with another can be captured, thus allowing a full representation of both direct and indirect causation on the aggregate results. This means that important new insights can be gained and hypotheses tested.


Assuntos
Resistência Microbiana a Medicamentos , Humanos , Resistência Microbiana a Medicamentos/genética , Antibacterianos/farmacologia , Modelos Teóricos , Bactérias/genética , Bactérias/efeitos dos fármacos , Interações Hospedeiro-Patógeno , Farmacorresistência Bacteriana/genética , Modelos Biológicos , Simulação por Computador
3.
Methods Mol Biol ; 2833: 79-91, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949703

RESUMO

Mathematical models have been used to study the spread of infectious diseases from person to person. More recently studies are developing within-host modeling which provides an understanding of how pathogens-bacteria, fungi, parasites, or viruses-develop, spread, and evolve inside a single individual and their interaction with the host's immune system.Such models have the potential to provide a more detailed and complete description of the pathogenesis of diseases within-host and identify other influencing factors that may not be detected otherwise. Mathematical models can be used to aid understanding of the global antibiotic resistance (ABR) crisis and identify new ways of combating this threat.ABR occurs when bacteria respond to random or selective pressures and adapt to new environments through the acquisition of new genetic traits. This is usually through the acquisition of a piece of DNA from other bacteria, a process called horizontal gene transfer (HGT), the modification of a piece of DNA within a bacterium, or through. Bacteria have evolved mechanisms that enable them to respond to environmental threats by mutation, and horizontal gene transfer (HGT): conjugation; transduction; and transformation. A frequent mechanism of HGT responsible for spreading antibiotic resistance on the global scale is conjugation, as it allows the direct transfer of mobile genetic elements (MGEs). Although there are several MGEs, the most important MGEs which promote the development and rapid spread of antimicrobial resistance genes in bacterial populations are plasmids and transposons. Each of the resistance-spread-mechanisms mentioned above can be modeled allowing us to understand the process better and to define strategies to reduce resistance.


Assuntos
Bactérias , Transferência Genética Horizontal , Bactérias/genética , Bactérias/efeitos dos fármacos , Humanos , Resistência Microbiana a Medicamentos/genética , Modelos Teóricos , Farmacorresistência Bacteriana/genética , Antibacterianos/farmacologia , Interações Hospedeiro-Patógeno/genética
4.
Methods Mol Biol ; 2833: 211-223, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38949713

RESUMO

Genomic sequencing has revolutionized microbial typing methods and transformed high-throughput methods in reference, clinical, and research laboratories. The detection of antimicrobial-resistant (AMR) determinants using genomic methods can provide valuable information on the emergence of resistance. Here we describe an approach to detecting AMR determinants using an open access and freely available platform which does not require bioinformatic expertise.


Assuntos
Biologia Computacional , Farmacorresistência Bacteriana , Genoma Bacteriano , Sequenciamento Completo do Genoma , Sequenciamento Completo do Genoma/métodos , Farmacorresistência Bacteriana/genética , Biologia Computacional/métodos , Humanos , Antibacterianos/farmacologia , Genômica/métodos , Software , Bactérias/genética , Bactérias/efeitos dos fármacos , Sequenciamento de Nucleotídeos em Larga Escala/métodos
5.
Subcell Biochem ; 104: 49-71, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38963483

RESUMO

Across living organisms, division is necessary for cell survival and passing heritable information to the next generation. For this reason, cell division is highly conserved among eukaryotes and prokaryotes. Among the most highly conserved cell division proteins in eukaryotes are tubulin and actin. Tubulin polymerizes to form microtubules, which assemble into cytoskeletal structures in eukaryotes, such as the mitotic spindle that pulls chromatids apart during mitosis. Actin polymerizes to form a morphological framework for the eukaryotic cell, or cytoskeleton, that undergoes reorganization during mitosis. In prokaryotes, two of the most highly conserved cell division proteins are the tubulin homolog FtsZ and the actin homolog FtsA. In this chapter, the functions of the essential bacterial cell division proteins FtsZ and FtsA and their roles in assembly of the divisome at the septum, the site of cell division, will be discussed. In most bacteria, including Escherichia coli, the tubulin homolog FtsZ polymerizes at midcell, and this step is crucial for recruitment of many other proteins to the division site. For this reason, both FtsZ abundance and polymerization are tightly regulated by a variety of proteins. The actin-like FtsA protein polymerizes and tethers FtsZ polymers to the cytoplasmic membrane. Additionally, FtsA interacts with later stage cell division proteins, which are essential for division and for building the new cell wall at the septum. Recent studies have investigated how actin-like polymerization of FtsA on the lipid membrane may impact division, and we will discuss this and other ways that division in bacteria is regulated through FtsZ and FtsA.


Assuntos
Proteínas de Bactérias , Divisão Celular , Proteínas do Citoesqueleto , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas do Citoesqueleto/metabolismo , Proteínas do Citoesqueleto/genética , Escherichia coli/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Bactérias/metabolismo , Bactérias/genética
6.
Subcell Biochem ; 104: 245-267, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38963490

RESUMO

Bacteria encode a wide range of survival and immunity systems, including CRISPR-Cas, restriction-modification systems, and toxin-antitoxin systems involved in defence against bacteriophages, as well as survival during challenging growth conditions or exposure to antibiotics. Toxin-antitoxin (TA) systems are small two- or three-gene cassettes consisting of a metabolic regulator (the "toxin") and its associated antidote (the "antitoxin"), which also often functions as a transcriptional regulator. TA systems are widespread in the genomes of pathogens but are also present in commensal bacterial species and on plasmids. For mobile elements such as plasmids, TA systems play a role in maintenance, and increasing evidence now points to roles of chromosomal toxin-antitoxin systems in anti-phage defence. Moreover, the widespread occurrence of toxin-antitoxin systems in the genomes of pathogens has been suggested to relate to survival during host infection as well as in persistence during antibiotic treatment. Upon repeated exposure to antibiotics, TA systems have been shown to acquire point mutations as well as more dramatic rearrangements such as in-frame deletions with potential relevance for bacterial survival and pathogenesis. In this review, we present an overview of the known functional and structural consequences of mutations and rearrangements arising in bacterial toxin-antitoxin systems and discuss their relevance for survival and persistence of pathogenic species.


Assuntos
Bactérias , Sistemas Toxina-Antitoxina , Sistemas Toxina-Antitoxina/genética , Bactérias/genética , Bactérias/metabolismo , Toxinas Bacterianas/genética , Toxinas Bacterianas/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo
7.
Sci Rep ; 14(1): 15096, 2024 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-38956049

RESUMO

Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the "biosynthesis process". Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.


Assuntos
Metagenoma , Metagenômica , Microbiota , Família Multigênica , Metabolismo Secundário , Microbiologia do Solo , Metagenômica/métodos , Microbiota/genética , Metabolismo Secundário/genética , Fazendas , Bactérias/genética , Bactérias/classificação , Bactérias/metabolismo , Etiópia , Filogenia
8.
Sci Rep ; 14(1): 15114, 2024 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-38956155

RESUMO

Wheat straw returning is a common agronomic measure in the farmland. Understanding organic carbon transformation is of great significance for carbon budget under the premise of widespread distribution of cadmium (Cd) contaminated soils. An incubation experiment was conducted to assess the influence of Cd contamination on the decomposition and accumulation of total organic carbon (TOC) as well as the composition and abundance of bacterial communities in eight soil types with wheat straw addition. The results showed that inhibition of Cd contamination on microbially mediated organic carbon decomposition was affected by soil types. The lower cumulative C mineralization and higher TOC content could be observed in the acidic soils relative to that in the alkaline soils. The content of Cd in soil exhibits different effects on the inhibition in decomposition of TOC. The high dosage level of Cd had stronger inhibitory impact due to its high toxicity. The decomposition of TOC was restricted by a reduction in soil bacterial abundance and weakening of bacterial activities. Redundancy analysis (RDA) indicated that Proteobacteria and Gemmatimonadetes were abundant in alkaline Cd-contaminated soils with wheat straw addition, while Bacteroidetes dominated cumulative C mineralization in acidic Cd-contamination soils. Moreover, the abundance of predicted functional bacteria indicated that high-dose Cd-contamination and acid environment all inhibited the decomposition of TOC. The present study suggested that pH played an important role on carbon dynamics in the Cd-contaminated soils with wheat straw addition.


Assuntos
Cádmio , Carbono , Microbiologia do Solo , Poluentes do Solo , Solo , Triticum , Cádmio/metabolismo , Cádmio/análise , Triticum/metabolismo , Triticum/química , Poluentes do Solo/análise , Poluentes do Solo/metabolismo , Carbono/metabolismo , Carbono/análise , Solo/química , Bactérias/metabolismo , Biodegradação Ambiental , Concentração de Íons de Hidrogênio
9.
Sci Rep ; 14(1): 15188, 2024 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-38956276

RESUMO

Wildlife harbour a diverse range of microorganisms that affect their health and development. Marsupials are born immunologically naïve and physiologically underdeveloped, with primary development occurring inside a pouch. Secretion of immunological compounds and antimicrobial peptides in the epithelial lining of the female's pouch, pouch young skin, and through the milk, are thought to boost the neonate's immune system and potentially alter the pouch skin microbiome. Here, using 16S rRNA amplicon sequencing, we characterised the Tasmanian devil pouch skin microbiome from 25 lactating and 30 non-lactating wild females to describe and compare across these reproductive stages. We found that the lactating pouch skin microbiome had significantly lower amplicon sequence variant richness and diversity than non-lactating pouches, however there was no overall dissimilarity in community structure between lactating and non-lactating pouches. The top five phyla were found to be consistent between both reproductive stages, with over 85% of the microbiome being comprised of Firmicutes, Proteobacteria, Fusobacteriota, Actinobacteriota, and Bacteroidota. The most abundant taxa remained consistent across all taxonomic ranks between lactating and non-lactating pouch types. This suggests that any potential immunological compounds or antimicrobial peptide secretions did not significantly influence the main community members. Of the more than 16,000 total identified amplicon sequence variants, 25 were recognised as differentially abundant between lactating and non-lactating pouches. It is proposed that the secretion of antimicrobial peptides in the pouch act to modulate these microbial communities. This study identifies candidate bacterial clades on which to test the activity of Tasmanian devil antimicrobial peptides and their role in pouch young protection, which in turn may lead to future therapeutic development for human diseases.


Assuntos
Lactação , Marsupiais , Microbiota , RNA Ribossômico 16S , Animais , Feminino , Marsupiais/microbiologia , RNA Ribossômico 16S/genética , Pele/microbiologia , Bactérias/classificação , Bactérias/genética
10.
BMC Microbiol ; 24(1): 235, 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38956452

RESUMO

BACKGROUND: Patients with pancreatic ductal adenocarcinoma (PDAC) display an altered oral, gastrointestinal, and intra-pancreatic microbiome compared to healthy individuals. However, knowledge regarding the bile microbiome and its potential impact on progression-free survival in PDACs remains limited. METHODS: Patients with PDAC (n = 45), including 20 matched pairs before and after surgery, and benign controls (n = 16) were included prospectively. The characteristics of the microbiomes of the total 81 bile were revealed by 16  S-rRNA gene sequencing. PDAC patients were divided into distinct groups based on tumor marker levels, disease staging, before and after surgery, as well as progression free survival (PFS) for further analysis. Disease diagnostic model was formulated utilizing the random forest algorithm. RESULTS: PDAC patients harbor a unique and diverse bile microbiome (PCoA, weighted Unifrac, p = 0.038), and the increasing microbial diversity is correlated with dysbiosis according to key microbes and microbial functions. Aliihoeflea emerged as the genus displaying the most significant alteration among two groups (p < 0.01). Significant differences were found in beta diversity of the bile microbiome between long-term PFS and short-term PFS groups (PCoA, weighted Unifrac, p = 0.005). Bacillota and Actinomycetota were identified as altered phylum between two groups associated with progression-free survival in all PDAC patients. Additionally, we identified three biomarkers as the most suitable set for the random forest model, which indicated a significantly elevated likelihood of disease occurrence in the PDAC group (p < 0.0001). The area under the receiver operating characteristic (ROC) curve reached 80.8% with a 95% confidence interval ranging from 55.0 to 100%. Due to the scarcity of bile samples, we were unable to conduct further external verification. CONCLUSION: PDAC is characterized by an altered microbiome of bile ducts. Biliary dysbiosis is linked with progression-free survival in all PDACs. This study revealed the alteration of the bile microbiome in PDACs and successfully developed a diagnostic model for PDAC.


Assuntos
Bile , Carcinoma Ductal Pancreático , Microbiota , Neoplasias Pancreáticas , Humanos , Carcinoma Ductal Pancreático/microbiologia , Carcinoma Ductal Pancreático/mortalidade , Carcinoma Ductal Pancreático/patologia , Bile/microbiologia , Masculino , Feminino , Neoplasias Pancreáticas/microbiologia , Neoplasias Pancreáticas/mortalidade , Neoplasias Pancreáticas/patologia , Microbiota/genética , Pessoa de Meia-Idade , Idoso , Disbiose/microbiologia , Intervalo Livre de Progressão , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Estudos Prospectivos , RNA Ribossômico 16S/genética
11.
Microbiome ; 12(1): 120, 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38956705

RESUMO

BACKGROUND: Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS: Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS: We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.


Assuntos
Bactérias , Biodiversidade , Glicosídeo Hidrolases , Polissacarídeos , Glicosídeo Hidrolases/metabolismo , Glicosídeo Hidrolases/genética , Polissacarídeos/metabolismo , Bactérias/genética , Bactérias/classificação , Bactérias/metabolismo , Ecossistema , Microbiota , Células Procarióticas/metabolismo , Células Procarióticas/classificação , Filogenia , Concentração de Íons de Hidrogênio
12.
Sci Adv ; 10(27): eadj7402, 2024 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-38959321

RESUMO

The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential abundance of taxa. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial unique molecular identifiers by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3' v3 and 5') as the best suited approach. We analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that up-regulate proinflammatory cytokines like IL1Β and CXCL8, while infected tumor cells up-regulate antigen processing and presentation pathways. These results show that myeloid cells with bacteria engulfed are a major source of bacterial RNA within the tumor microenvironment (TME) and may inflame the TME and influence immunotherapy response.


Assuntos
Bactérias , RNA-Seq , Análise de Célula Única , Humanos , Análise de Célula Única/métodos , RNA-Seq/métodos , Bactérias/genética , Microambiente Tumoral , Células Mieloides/metabolismo , Células Mieloides/microbiologia , Análise de Sequência de RNA/métodos , Neoplasias Colorretais/microbiologia , Neoplasias Colorretais/genética , Biologia Computacional/métodos , RNA Bacteriano/genética , Neoplasias Esofágicas/microbiologia , Neoplasias Esofágicas/genética , Microbiota , Análise da Expressão Gênica de Célula Única
13.
Eur Respir Rev ; 33(173)2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38960615

RESUMO

Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.


Assuntos
Bronquiectasia , Disbiose , Interações Hospedeiro-Patógeno , Microbiota , Bronquiectasia/microbiologia , Bronquiectasia/imunologia , Humanos , Pulmão/microbiologia , Animais , Fatores de Risco , Bactérias/genética , Bactérias/classificação , Infecções Respiratórias/microbiologia , Infecções Respiratórias/imunologia , Prognóstico
14.
Front Cell Infect Microbiol ; 14: 1420995, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38962321

RESUMO

Introduction: Due to the high-density farming of Larimichthys crocea over the years, diseases caused by pathogens such as bacteria, viruses, and parasites frequently occur in Ningbo, posing a huge threat and challenge to the sustainable and healthy development of the L. crocea's bay farming industry. In order to understand the diseases occurrence in L. crocea farming in Ningbo area, an epidemiological investigation of L. crocea diseases was carried out through regular sampling in 2023. Methods: From April to October 2023, routine sampling of L. crocea was conducted monthly in various farming areas in Ningbo. Each time, live or dying L. crocea with obvious clinical symptoms were sampled, with a total number of 55 L. crocea collected. The samples were preserved in ice bags and transported to the laboratory for pathogen detection(including bacterial isolation and identification,virus identification, and parasites detection). Results: A total of fifty-five fish dying L. crocea with obvious clinical symptoms were collected in this study, of which 78.18% (43/55) were detected with symptoms caused by pathogenic infection, while 21.82% (12/55) did not have identified pathogens, which were presumed to be breeding abrasions, nutritional metabolic disorders, unconventional pathogens infection or other reasons. A total of twenty-five pathogenic bacteria strains were isolated, which mainly were Pseudomonas plecoglossicida and Vibrio harveyi, accounting for 52% (13/25) and 32% (8/25) of the pathogenic bacteria strains, respectively. Among them, both V. harveyi and Streptococcus. iniae co-infected one fish. Additionally, three other bacterial strains including Nocardia seriolae, Staphylococcus Saprophyticus, and Photobacterium damselae subsp.damselae were isolated. Microscopic examination mainly observed two parasites, Cryptocaryon irritans and Neobenedenia girellae. In virus detection, the red sea bream iridovirus (RSIV) was mainly detected in L. crocea. Statistical analysis showed that among the fish with detected pathogens, 55.81% (24/43) had bacterial infections, 37.21% (16/43) had parasitic infections, and 37.21% (16/43) had RSIV infections. Among them, five fish had mixed infections of bacteria and parasites, three had mixed infections of bacteria and viruses, three had mixed infections of parasites and viruses, and one L. crocea had mixed infections of viruses, bacteria, and parasites. Discussion: These findings indicate that these three major types of diseases are very common in the L. crocea farming area in Ningbo, implying the complexity of mixed infections of multiple diseases.


Assuntos
Doenças dos Peixes , Perciformes , Animais , Doenças dos Peixes/epidemiologia , Doenças dos Peixes/parasitologia , Doenças dos Peixes/microbiologia , Perciformes/microbiologia , Perciformes/parasitologia , China/epidemiologia , Aquicultura , Vibrio/isolamento & purificação , Vibrio/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Bactérias/genética
15.
Appl Microbiol Biotechnol ; 108(1): 402, 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38951204

RESUMO

Delayed graft function (DGF) is a frequently observed complication following kidney transplantation (KT). Our prior research revealed dynamic shifts in salivary microbiota post-KT with immediate graft function (IGF), yet its behavior during DGF remains unexplored. Five recipients with DGF and 35 recipients with IGF were enrolled. Saliva samples were collected during the perioperative period, and 16S rRNA gene sequencing was performed. The salivary microbiota of IGFs changed significantly and gradually stabilized with the recovery of renal function. The salivary microbiota composition of DGFs was significantly different from that of IGFs, although the trend of variation appeared to be similar to that of IGFs. Salivary microbiota that differed significantly between patients with DGF and IGF at 1 day after transplantation were able to accurately distinguish the two groups in the randomForest algorithm (accuracy = 0.8333, sensitivity = 0.7778, specificity = 1, and area under curve = 0.85), with Selenomonas playing an important role. Bacteroidales (Spearman's r = - 0.4872 and p = 0.0293) and Veillonella (Spearmen's r = - 0.5474 and p = 0.0125) were significantly associated with the serum creatinine in DGF patients. Moreover, the significant differences in overall salivary microbiota structure between DGF and IGF patients disappeared upon long-term follow-up. This is the first study to investigate the dynamic changes in salivary microbiota in DGFs. Our findings suggested that salivary microbiota was able to predict DGF in the early stages after kidney transplantation, which might help the perioperative clinical management and early-stage intervention of kidney transplant recipients. KEY POINTS: • Salivary microbiota on the first day after KT could predict DGF. • Alterations in salivary taxa after KT are related to recovery of renal function.


Assuntos
Função Retardada do Enxerto , Transplante de Rim , Microbiota , RNA Ribossômico 16S , Saliva , Humanos , Transplante de Rim/efeitos adversos , Saliva/microbiologia , Masculino , Feminino , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Adulto , Bactérias/classificação , Bactérias/isolamento & purificação , Bactérias/genética
17.
World J Microbiol Biotechnol ; 40(9): 264, 2024 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-38990244

RESUMO

Bentonite is an integral part of the engineered barrier system (EBS) in deep geological repositories (DGR) for nuclear waste, but its indigenous microorganisms may jeopardize long-term EBS integrity. To predict microbial activity in DGRs, it is essential to understand microbial reactions to the early hot phase of DGR evolution. Two bentonites (BCV and MX-80) with varied bentonite/water ratios and saturation levels (compacted to 1600 kg.m- 3 dry density/powder/suspension), were subjected to heat (90-150 °C) and irradiation (0.4 Gy.h- 1) in the long-term experiments (up to 18 months). Molecular-genetic, microscopic, and cultivation-based techniques assessed microbial survivability. Exposure to 90 °C and 150 °C notably diminished microbial viability, irrespective of bentonite form, with negligible impacts from irradiation or sample type compared to temperature. Bentonite powder samples exhibited microbial recovery after 90 °C heating for up to 6 months but not 12 months in most cases; exposure to 150 °C had an even stronger effect. Further long-term experiments at additional temperatures combined with the mathematical prediction of temperature evolution in DGR are recommended to validate the possible evolution and spatial distribution of microbially depleted zones in bentonite buffer around the waste canisters and refine predictions of microbial effects over time in the DGR.


Assuntos
Bactérias , Bentonita , Raios gama , Temperatura Alta , Viabilidade Microbiana , Bentonita/química , Viabilidade Microbiana/efeitos da radiação , Bactérias/classificação , Bactérias/efeitos da radiação , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Resíduos Radioativos/análise , Microbiologia do Solo
18.
Appl Microbiol Biotechnol ; 108(1): 411, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38980443

RESUMO

This study investigates the dynamic changes in milk nutritional composition and microbial communities in Tibetan sheep and goats during the first 56 days of lactation. Milk samples were systematically collected at five time points (D0, D7, D14, D28, D56) post-delivery. In Tibetan sheep, milk fat, protein, and casein contents were highest on D0, gradually decreased, and stabilized after D14, while lactose and galactose levels showed the opposite trend. Goat milk exhibited similar initial peaks, with significant changes particularly between D0, D7, D14, and D56. 16S rRNA gene sequencing revealed increasing microbial diversity in both species over the lactation period. Principal coordinates analysis identified distinct microbial clusters corresponding to early (D0-D7), transitional (D14-D28), and mature (D56) stages. Core phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, dominated the milk microbiota, with significant temporal shifts. Core microbes like Lactobacillus, Leuconostoc, and Streptococcus were common in both species, with species-specific taxa observed (e.g., Pediococcus in sheep, Shewanella in goats). Furthermore, we observed a highly shared core microbiota in sheep and goat milk, including Lactobacillus, Leuconostoc, and Streptococcus. Spearman correlation analysis highlighted significant relationships between specific microbial genera and milk nutrients. For instance, Lactobacillus positively correlated with total solids, non-fat milk solids, protein, and casein, while Mannheimia negatively correlated with protein content. This study underscores the complex interplay between milk composition and microbial dynamics in Tibetan sheep and goats, informing strategies for livestock management and nutritional enhancement. KEY POINTS: • The milk can be classified into three types based on the microbiota composition • The changes of milk microbiota are closely related to the variations in nutrition • Filter out microbiota with species specificity and age specificity in the milk.


Assuntos
Cabras , Microbiota , Leite , RNA Ribossômico 16S , Animais , Cabras/microbiologia , Leite/microbiologia , Leite/química , Ovinos/microbiologia , RNA Ribossômico 16S/genética , Tibet , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Feminino , Lactação , Caseínas , Proteínas do Leite/análise
19.
Sci Rep ; 14(1): 15838, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38982048

RESUMO

Cryoconites are the deposits on the surface of glaciers that create specific ecological niches for the development of microorganism communities. The sediment material can vary in origin, structure, and nutrient content, creating local variations in the growth conditions. An additional factor of variability is the location of the glaciers, as they are found in different climatic zones in the high mountain regions and closer to the poles. Here, using the analysis of amplicon sequencing of the 16S rRNA gene, we studied the taxonomic composition of the prokaryotic communities from glaciers from remote regions, including the Arctic (Mushketova on the Severnaya Zemlya, IGAN in Polar Ural), Antarctic (Pimpirev on the Livingstone Island) and Central Caucasus (Skhelda and Garabashi) and connected it with the variation of the physicochemical characteristics of the substrate: pH, carbon, nitrogen, macro- and microelements. The cryoconite microbiomes were comprised of specific for this environment phyla (mostly Pseudomonadota, Cyanobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota), but each glacier had a unique taxonomic imprint. The core microbiome between regions was composed of only a few ASVs, among which the most likely globally distributed ones attributed to Polaromonas sp., Rhodoferax sp., Cryobacterium sp., and Hymenobacter frigidus. The WGSNA defined clusters of co-occurring ASVs between microbiomes, that significantly change their abundance corresponding with the variation of chemical parameters of cryoconites, but do not fully coincide with their regional separation. Thus, our work demonstrates that the chemical characteristics of the sediment material can explain the variation in the cryoconite prokaryotic community which is not always linked to geographic isolation.


Assuntos
Camada de Gelo , Microbiota , RNA Ribossômico 16S , Regiões Árticas , Regiões Antárticas , Camada de Gelo/microbiologia , RNA Ribossômico 16S/genética , Microbiota/genética , Sedimentos Geológicos/microbiologia , Bactérias/genética , Bactérias/classificação , Filogenia
20.
J Appl Microbiol ; 135(7)2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38982332

RESUMO

AIMS: A severe lockdown occurred in Wuhan during the COVID-19 pandemic, followed by a remission phase in the pandemic's aftermath. This study analyzed the bacterial and fungal profiles of respiratory pathogens in patients hospitalized with non-COVID-19 lower respiratory tract infections (LRTIs) during this period to determine the pathogen profile distributions in different age groups and hospital departments in Wuhan. METHODS AND RESULTS: We collected reports of pathogen testing in the medical records of patients hospitalized with non-COVID-19 LRTI between 2019 and 2021. These cases were tested for bacterial and fungal pathogens using 16S and internal transcribed spacer sequencing methods on bronchoalveolar lavage fluid samples. The study included 1368 cases. The bacteria most commonly identified were Streptococcus pneumoniae (12.50%) and Mycoplasma pneumoniae (8.33%). The most commonly identified fungi were Aspergillus fumigatus (2.49%) and Pneumocystis jirovecii (1.75%). Compared to 2019, the S. pneumoniae detection rates increased significantly in 2021, and those of M. pneumoniae decreased. Streptococcus pneumoniae was detected mainly in children. The detection rates of almost all fungi were greater in the respiratory Intensive Care Unit compared to respiratory medicine. Streptococcus pneumoniae and M. pneumoniae were detected more frequently in the pediatric department. CONCLUSIONS: Before and after the COVID-19 outbreak, a change in the common pathogen spectrum was detected in patients with non-COVID-19 in Wuhan, with the greatest change occurring among children. The major pathogens varied by the patient's age and the hospital department.


Assuntos
COVID-19 , Hospitalização , Infecções Respiratórias , Humanos , China/epidemiologia , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Infecções Respiratórias/epidemiologia , Pessoa de Meia-Idade , Criança , Masculino , Adulto , Feminino , Pré-Escolar , Adolescente , Idoso , Lactente , COVID-19/epidemiologia , Fungos/isolamento & purificação , Fungos/genética , Fungos/classificação , Adulto Jovem , Streptococcus pneumoniae/isolamento & purificação , Streptococcus pneumoniae/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Bactérias/genética , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Mycoplasma pneumoniae/isolamento & purificação , Mycoplasma pneumoniae/genética , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia
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