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Advances in Biochemical... 2020Alkaliphilic microorganisms are ubiquitous and inhabit various econiches on Earth. Alkaline environments suitable for alkaliphilic microbial communities may be created...
Alkaliphilic microorganisms are ubiquitous and inhabit various econiches on Earth. Alkaline environments suitable for alkaliphilic microbial communities may be created by certain geological processes or human activities. Moreover, a significant contribution to the emergence of alkaline conditions may be due to the activity of neutralophilic microorganisms through certain reactions, which explains the widespread distribution of alkaliphiles. Alkaliphilic microorganisms are part of extremophiles and become interesting and useful in environmental and industrial microbiology. With increasing knowledge of alkaliphiles, we greatly increase their biotechnological and industrial application potential. New microorganisms from natural habitats serve as a practically endless source of new enzymes. This chapter summarizes the scattered data on alkaliphiles isolated from habitats other than soda lakes. The conditions for occurrence of alkaline habitats are also considered. Moreover, the chapter reviews some important features on preparation of media for the isolation and cultivation of alkaliphiles. The chapter also includes relevant information on chromatographic analysis of alkaliphiles culture. Graphical Abstract.
Topics: Hydrogen-Ion Concentration; Industrial Microbiology
PubMed: 30796504
DOI: 10.1007/10_2018_84 -
BMC Microbiology Jun 2021Phages are one of the key components in the structure, dynamics, and interactions of microbial communities in different bins. It has a clear impact on human health and... (Review)
Review
Phages are one of the key components in the structure, dynamics, and interactions of microbial communities in different bins. It has a clear impact on human health and the food industry. Bacteriophage characterization using in vitro approaches are time/cost consuming and laborious tasks. On the other hand, with the advent of new high-throughput sequencing technology, the development of a powerful computational framework to characterize the newly identified bacteriophages is inevitable for future research. Machine learning includes powerful techniques that enable the analysis of complex datasets for knowledge discovery and pattern recognition. In this study, we have conducted a comprehensive review of machine learning methods application using different types of features were applied in various aspects of bacteriophage research including, automated curation, identification, classification, host species recognition, virion protein identification, and life cycle prediction. Moreover, potential limitations and advantages of the developed frameworks were discussed.
Topics: Bacteriophages; Machine Learning; Virology
PubMed: 34174831
DOI: 10.1186/s12866-021-02256-5 -
Clinical Microbiology and Infection :... Nov 2023
Topics: Humans; Microbiology; Mentors; Communicable Diseases
PubMed: 37532128
DOI: 10.1016/j.cmi.2023.07.028 -
Briefings in Bioinformatics Sep 2021Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved... (Review)
Review
Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
Topics: DNA Barcoding, Taxonomic; Feces; Genitalia; Genome, Microbial; High-Throughput Nucleotide Sequencing; Humans; Metagenome; Metagenomics; Microbiota; Mouth; Sequence Analysis, DNA; Skin; Soil Microbiology; Water Microbiology
PubMed: 33758906
DOI: 10.1093/bib/bbab030 -
MBio May 2024In this editorial, I share advice and general principles based on recent experiences as a mentor and evaluator for early-career microbiology and immunology faculty...
In this editorial, I share advice and general principles based on recent experiences as a mentor and evaluator for early-career microbiology and immunology faculty seeking promotion and tenure. I outline 10 recommendations covering research, service, teaching, and mentoring. In addition, I encourage nuanced conversations with colleagues to strategically navigate the unique promotion and tenure processes at different institutions. I hope that these practical tips will assist early-career faculty in attaining promotion and tenure, contributing to long-term scientific and career advances.
Topics: Microbiology; Humans; Allergy and Immunology; Career Mobility; Faculty; Mentoring; Mentors
PubMed: 38551369
DOI: 10.1128/mbio.00631-24 -
Advances in Parasitology 2021Enterocytozoon bieneusi is a microsporidian microorganism that causes intestinal disease in animals including humans. E. bieneusi is an obligate intracellular pathogen,... (Review)
Review
Enterocytozoon bieneusi is a microsporidian microorganism that causes intestinal disease in animals including humans. E. bieneusi is an obligate intracellular pathogen, typically causing severe or chronic diarrhoea, malabsorption and/or wasting. Currently, E. bieneusi is recognised as a fungus, although its exact classification remains contentious. The transmission of E. bieneusi can occur from person to person and/or animals to people. Transmission is usually via the faecal-oral route through E. bieneusi spore-contaminated water, environment or food, or direct contact with infected individuals. Enterocytozoon bieneusi genotypes are usually identified and classified by PCR-based sequencing of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA. To date, ~600 distinct genotypes of E. bieneusi have been recorded in ~170 species of animals, including various orders of mammals and reptiles as well as insects in >40 countries. Moreover, E. bieneusi has also been found in recreational water, irrigation water, and treated raw- and waste-waters. Although many studies have been conducted on the epidemiology of E. bieneusi, prevalence surveys of animals and humans are scant in some countries, such as Australia, and transmission routes of individual genotypes and related risk factors are poorly understood. This article/chapter reviews aspects of the taxonomy, biology and epidemiology of E. bieneusi; the diagnosis, treatment and prevention of microsporidiosis; critically appraises the naming system for E. bieneusi genotypes as well as the phylogenetic relationships of these genotypes; provides new insights into the prevalence and genetic composition of E. bieneusi populations in animals in parts of Australia using molecular epidemiological tools; and proposes some areas for future research in the E. bieneusi/microsporidiosis field.
Topics: Animals; Enterocytozoon; Food Microbiology; Humans; Microsporidiosis; Prevalence; Water Microbiology; Zoonoses
PubMed: 33482973
DOI: 10.1016/bs.apar.2020.10.001 -
Journal of the American Dental... Nov 2020
Topics: Aerosols; Air Microbiology; Humans
PubMed: 33121602
DOI: 10.1016/j.adaj.2020.09.016 -
Trends in Biotechnology Feb 2021Microbial bioremediation based on nano- to micrometer-scale electron transport has been intensively studied during the past decade, but its application can be hindered... (Review)
Review
Microbial bioremediation based on nano- to micrometer-scale electron transport has been intensively studied during the past decade, but its application can be hindered by a deficiency of suitable electron acceptors or slow mass transportation at contaminated sites. Microbial long-distance electron transport (LDET), which can couple spatially separated redox reactions across distances in natural environments, has recently emerged at centimeter-length scales. LDET explains a range of globally important biogeochemical phenomena and overcomes the drawbacks of conventional bioremediation by directly linking distant electron donors and acceptors. Here, we highlight recent research outcomes in examining, characterizing, and engineering LDET, and describe how LDET can be exploited to develop advanced technologies for the bioremediation of soils and sediments.
Topics: Biodegradation, Environmental; Electron Transport; Geologic Sediments; Oxidation-Reduction; Soil Microbiology
PubMed: 32680591
DOI: 10.1016/j.tibtech.2020.06.011 -
Current Opinion in Plant Biology Jun 2023The rhizosphere is the soil-plant interface colonized by bacterial and fungal species that exert growth-promoting and adaptive benefits. The plant-bacteria relationships... (Review)
Review
The rhizosphere is the soil-plant interface colonized by bacterial and fungal species that exert growth-promoting and adaptive benefits. The plant-bacteria relationships rely upon the perception of volatile organic compounds (VOCs), canonical phytohormones such as auxins and cytokinins, and the bacterial quorum sensing-related N-acyl-L-homoserine lactones and cyclodipeptides. On the other hand, plant-beneficial Trichoderma fungi emit highly active VOCs, including 6-pentyl-2H-pyran-2-one (6-PP), and β-caryophyllene, which contribute to plant morphogenesis, but also into how these microbes spread over roots or live as endophytes. Here, we describe recent findings concerning how compounds from beneficial bacteria and fungi affect root architecture and advance into the signaling events that mediate microbial recognition.
Topics: Rhizosphere; Plant Development; Plant Growth Regulators; Bacteria; Plants; Fungi; Volatile Organic Compounds; Plant Roots; Soil Microbiology
PubMed: 36716513
DOI: 10.1016/j.pbi.2023.102336 -
Clinics in Laboratory Medicine Dec 2020Formal medical and public health microbiology (MPHM) fellowship programs play a key role in preparing future clinical microbiology laboratory directors for their... (Review)
Review
Formal medical and public health microbiology (MPHM) fellowship programs play a key role in preparing future clinical microbiology laboratory directors for their leadership and management responsibilities. Given the continually evolving MPHM field, fellowships must remain adaptable to changes in the field, providing trainees with the opportunity to engage with newly emerging diagnostic modalities, while continuing to emphasize the "bread and butter" techniques of clinical microbiology. This article discusses the key components of a fellowship program and provides recommendations for incorporating educational best practices.
Topics: Fellowships and Scholarships; Humans; Laboratories; Medical Laboratory Science; Microbiology
PubMed: 33121620
DOI: 10.1016/j.cll.2020.08.009