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Journal of Microbiological Methods Dec 2022Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are... (Review)
Review
Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.
Topics: Animals; Bacteria; Fishes; Food Microbiology; Meat; Proteomics; RNA, Ribosomal, 16S
PubMed: 36243229
DOI: 10.1016/j.mimet.2022.106599 -
Frontiers in Immunology 2020The term ocular microbiota refers to all types of commensal and pathogenic microorganisms present on or in the eye. The ocular surface is continuously exposed to the...
The term ocular microbiota refers to all types of commensal and pathogenic microorganisms present on or in the eye. The ocular surface is continuously exposed to the environment and harbors various commensals. Commensal microbes have been demonstrated to regulate host metabolism, development of immune system, and host defense against pathogen invasion. An unbalanced microbiota could lead to pathogenic microbial overgrowth and cause local or systemic inflammation. The specific antigens that irritate the deleterious immune responses in various inflammatory eye diseases remain obscure, while recent evidence implies a microbial etiology of these illnesses. The purpose of this review is to provide an overview of the literature on ocular microbiota and the role of commensal microbes in several eye diseases. In addition, this review will also discuss the interaction between microbial pathogens and host factors involved in intraocular inflammation, and evaluate therapeutic potential of targeting ocular microbiota to treat intraocular inflammation.
Topics: Animals; Eye; Eye Diseases; Humans; Immune System; Immunity; Inflammation; Microbiota
PubMed: 33424865
DOI: 10.3389/fimmu.2020.609765 -
Yeast (Chichester, England) Jun 2022The plant phyllosphere is one of the largest sources of microorganisms, including yeasts. In bromeliads, the knowledge of yeasts is dispersed and still incipient. To... (Review)
Review
The plant phyllosphere is one of the largest sources of microorganisms, including yeasts. In bromeliads, the knowledge of yeasts is dispersed and still incipient. To understand the extent of our knowledge of the subject, this review proposes to compile and synthesize existing knowledge, elucidating possible patterns, biotechnological and taxonomic potentials, bringing to light new knowledge, and identifying information gaps. For such, we systematically review scientific production on yeasts in bromeliads using various databases. The results indicated that the plant compartments flowers, fruits, leaves, and water tank (phytotelma) have been studied when focusing on the yeast community in the bromeliad phyllosphere. More than 180 species of yeasts and yeast-like fungi were recorded from the phyllosphere, 70% were exclusively found in one of these four compartments and only 2% were shared among all. In addition, most of the community had a low frequency of occurrence, and approximately half of the species had a single record. Variables such as bromeliad subfamilies and functional types, as well as plant compartments, were statistically significant, though inconclusive and with low explanatory power. At least 50 yeast species with some biotechnological potentials have been isolated from bromeliads. More than 90% of these species were able to produce extracellular enzymes. In addition, other biotechnological applications have also been recorded. Moreover, new species have been described, though yeasts were only exploited in approximately 1% of the existing bromeliads species, which highlights that there is still much to be explored. Nevertheless, it appears that we are still far from recovering the completeness of the diversity of yeasts in this host. Furthermore, bromeliads proved to be a good ecological model for prospecting new yeasts and for studies on the interaction between plants and yeasts. In addition, the yeast community diverged among plant compartments, establishing bromeliads as a microbiologically complex and heterogeneous mosaic.
Topics: Bromeliaceae; Flowers; Plants; Water; Yeasts
PubMed: 35715939
DOI: 10.1002/yea.3804 -
Journal de Mycologie Medicale Apr 2020Limited data are available on the epidemiology and etiology of cryptococcal infections in the Middle East. We aimed to conduct the systematic review and meta-analysis to... (Meta-Analysis)
Meta-Analysis
OBJECTIVE
Limited data are available on the epidemiology and etiology of cryptococcal infections in the Middle East. We aimed to conduct the systematic review and meta-analysis to summarize the epidemiological data on prevalence of Cryptococcus species complexes in trees and their surroundings, bird guano and secretions, animals, and highlight the reported episodes of cryptococcosis in Iran.
MATERIALS AND METHODS
Twelve databases, including PubMed, Science Direct, Scopus, Proquest, Google Scholar, Embase, and the ISI Web of Science, as well as the national databases, from January 1969 to October 2019 were searched. Furthermore, gray literature (e.g., thesis, congress abstracts) was evaluated using Iran Doc and www.thesis.
RESEARCH
ac.ir. Search process was accomplished on English or Persian language articles using the following keywords: "Cryptococcus", "Cryptococcosis", "invasive fungal infection", "Humans", "Birds", "Pigeon", "Animals", "Tree", "Eucalyptus", and "Iran", both alone and in combination.
RESULTS
Overall 36 studies were eligible regarding Cryptococcus and cryptococcosis in Iran. The total prevalence rates of Cryptococcus species in the tree was 4.7% (95% CI: 2.3-7.8), and in bird guano was 20.4% (95% CI: 10.7-32.2). Cryptococcosis in animal, and human were 1.7% (95% CI: 0.01-5.1), and 2.8% (95% CI: 0.7v6.1), respectively. The highest prevalence of Cryptococcus in the trees (14.6%), and bird guano (89.4%) in Khorasan, animals (8.9%) in Chaharmahal and Bakhtiari, and human (4.4%) in Mazandaran provinces were reported.
CONCLUSIONS
Given the significant risk of Cryptococcus species for susceptible humans, mainly HIV-infected patients, it seems quite necessary to adopt concrete preventive strategies to pinpoint the environmental habitats of this yeast.
Topics: Animals; Bird Diseases; Columbidae; Cryptococcosis; Cryptococcus; Eucalyptus; Humans; Invasive Fungal Infections; Iran; Plant Diseases; Prevalence; Trees
PubMed: 31864801
DOI: 10.1016/j.mycmed.2019.100917 -
European Journal of Clinical... Jul 2016Staphylococcus aureus might amplify symptoms in chronic inflammatory skin diseases. This study evaluates skin and mucosal colonization with S. aureus in patients with... (Meta-Analysis)
Meta-Analysis Review
Staphylococcus aureus might amplify symptoms in chronic inflammatory skin diseases. This study evaluates skin and mucosal colonization with S. aureus in patients with psoriasis, acne and rosacea. A systematic literature search was conducted. Both odds ratios (OR) for colonization in patients versus controls and the prevalence of colonization in patients are reported. Fifteen articles about psoriasis and 13 about acne (12 having a control group) were included. No study in rosacea met our inclusion criteria. For psoriasis, one study out of three controlled studies showed increased skin colonization (OR 18.86; 95 % confidence interval [CI] 2.20-161.99). Three out of the five studies that reported on nasal colonization showed significant ORs varying from 1.73 (95 % CI 1.16-2.58) to 14.64 (95 % CI 2.82-75.95). For acne one of the three studies that evaluated skin colonization reported a significant OR of 4.16 (95 % CI 1.74-9.94). A relation between nasal colonization and acne was not found. Limitations in study design and low sample sizes should be taken into consideration when interpreting the results. Colonisation with S. aureus seems to be increased in patients with psoriasis. This bacterial species, known for its potential to induce long-lasting inflammation, might be involved in psoriasis pathogenesis. Information on acne is limited. Prospective controlled studies should further investigate the role of S. aureus in chronic inflammatory skin diseases.
Topics: Acne Vulgaris; Carrier State; Case-Control Studies; Humans; Mucous Membrane; Odds Ratio; Psoriasis; Rosacea; Skin; Staphylococcal Infections; Staphylococcus aureus
PubMed: 27151386
DOI: 10.1007/s10096-016-2647-3 -
American Journal of Infection Control Nov 2016Worldwide, enteric viruses are the main cause of acute gastroenteritis. In humans, these viruses spread via person-to-person contact, food, water, and/or the... (Review)
Review
BACKGROUND
Worldwide, enteric viruses are the main cause of acute gastroenteritis. In humans, these viruses spread via person-to-person contact, food, water, and/or the environment. Their survival and inactivation on hard surfaces have been extensively studied; however, nonlaunderable soft surfaces, such as upholstery and carpet, have received little attention. The aim of this systematic review was to determine factors that influence the survival and inactivation of enteric viruses on nonlaunderable soft surfaces.
METHODS
EBSCO and Web of Science were searched for experimental studies published between 1965 and 2015 using Preferred Reporting Items for Systematic Reviews and Meta-Analyses methods. Titles and abstracts were screened using 3 eligibility criteria. The quality of all study methods was also assessed.
RESULTS
Our search yielded 12 articles. Viruses survived between 0 hours and 140 days depending on surface and environment conditions. Virus survival was influenced by temperature, relative humidity, organic content, and deposition method. A variety of chemistries were tested across studies and were shown to have a varied effect on enteric viruses. Chlorine, glutaraldehyde, vaporous ozone, and hydrogen peroxide were the most efficacious against enteric viruses (> 3-log reduction).
CONCLUSIONS
Environmental factors, such as temperature and relative humidity, can influence survival of enteric viruses on nonlaunderable soft surfaces. The efficacy of liquid and vaporous chemistries are associated with surface and virus type.
Topics: Environmental Microbiology; Microbial Viability; Norovirus; Rotavirus
PubMed: 27160982
DOI: 10.1016/j.ajic.2016.03.018 -
Journal of Infection and Public Health Oct 2023The newly discovered coronavirus SARS-CoV-2 has sparked a worldwide pandemic of COVID-19, which has caused havoc on medical infrastructures, economies, and cultures... (Meta-Analysis)
Meta-Analysis Review
The newly discovered coronavirus SARS-CoV-2 has sparked a worldwide pandemic of COVID-19, which has caused havoc on medical infrastructures, economies, and cultures around the world. Determining the whole scenario is essential since SARS-CoV-2 variants and sub-variants keep appearing after vaccinations and booster doses. The objective of this secondary meta-analysis is to analysis co-infection, secondary infections, and antimicrobial resistance (AMR) in COVID-19 patients. This study used five significant databases to conduct a systematic review and an overlap meta-analysis to evaluate the pooled estimates of co-infections and secondary infections. The summary of the meta-analysis showed an overall co-infection effect of 26.19% (95% confidence intervals CI: 21.39-31.01, I =98.78, n = 14 meta-analysis) among patients with COVID-19. A coinfection effect of 11.13% (95% CI: 9.7-12.56, I =99.14, n = 11 meta-analysis) for bacteria; 9.69% (95% CI: 1.21-7.90, I =98.33) for fungal and 3.48% (95% CI: 2.15-4.81, I =95.84) for viruses. A secondary infection effect of 19.03% (95% CI: 9.53-28.54, I =85.65) was pooled from 2 meta-analyses (Ave: 82 primary studies). This is the first study that compiles the results of all the previous three years meta-analyses into a single source and offers strong proof of co-infections and secondary infections in COVID-19 patients. Early detection of co-infection and AMR is crucial for COVID-19 patients in order to effective treatment.
Topics: Humans; COVID-19; Coinfection; SARS-CoV-2; Anti-Bacterial Agents; Drug Resistance, Bacterial
PubMed: 37572572
DOI: 10.1016/j.jiph.2023.07.005 -
FEMS Microbiology Reviews Jan 2024Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer...
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
Topics: Alphaproteobacteria; Bacteria; Plant Roots; Rhizosphere; Soil Microbiology; Symbiosis
PubMed: 38093453
DOI: 10.1093/femsre/fuad066 -
Fish Physiology and Biochemistry Dec 2021Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for... (Review)
Review
Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.
Topics: Animals; Fishes; Gastrointestinal Microbiome; Intestines
PubMed: 34750711
DOI: 10.1007/s10695-021-01027-3 -
Minerva Stomatologica Dec 2018The association between the oral microbiome and periodontal diseases is still unclear. We performed a systematic review and meta-analysis to quantify the association... (Meta-Analysis)
Meta-Analysis
INTRODUCTION
The association between the oral microbiome and periodontal diseases is still unclear. We performed a systematic review and meta-analysis to quantify the association between the specific pathogens and periodontitis.
EVIDENCE ACQUISITION
A computerized medical search was performed using MEDLINE and SCOPUS database between 1950 and May 2017 to identify all case-control studies that evaluated the association between specific pathogens and periodontitis. The pooled Odds Ratio with relative 95% confidence interval (95% CI) was calculated and plotted in the forest plot.
EVIDENCE SYNTHESIS
Eleven RCTs involving 2111 patients were included. The retrieved case-control studies evaluated the presence or absence of different targeted pathogens. Among the microrganisms evaluated Porphyromonas gengivalis (OR [95% CI] 2.93 [0.98,8.87]; P<0.0001) and Streptococcus mutans (OR [95% CI] 1.77 [0.89-3.54]; P=0.03) were found to be risk factors for the development of periodontitis, while Aggregatibacter actinomycetemcomitans (OR [95% CI] 0.52 [0.33-0.83]) played a protective role for periodontitis.
CONCLUSIONS
It seems that changes in the taxonomic composition of the microbiome rather than single targeted pathogens is the key determinant of periodontitis.
Topics: Humans; Microbiota; Periodontitis
PubMed: 30207437
DOI: 10.23736/S0026-4970.18.04198-5