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Applied Microbiology and Biotechnology Aug 2020Modernisation of our households created novel opportunities for microbial growth and thus changed the array of microorganisms we come in contact with. While many studies... (Review)
Review
Modernisation of our households created novel opportunities for microbial growth and thus changed the array of microorganisms we come in contact with. While many studies have investigated microorganisms in the air and dust, tap water, another major input of microbial propagules, has received far less attention. The quality of drinking water in developed world is strictly regulated to prevent immediate danger to human health. However, fungi, algae, protists and bacteria of less immediate concern are usually not screened for. These organisms can thus use water as a vector of transmission into the households, especially if they are resistant to various water treatment procedures. Good tolerance of unfavourable abiotic conditions is also important for survival once microbes enter the household. Limitation of water availability, high or low temperatures, application of antimicrobial chemicals and other measures are taken to prevent indoor microbial overgrowth. These conditions, together with a large number of novel chemicals in our homes, shape the diversity and abundance of indoor microbiota through constant selection of the most resilient species, resulting in a substantial overlap in diversity of indoor and natural extreme environments. At least in fungi, extremotolerance has been linked to human pathogenicity, explaining why many species found in novel indoor habitats (such as dishwasher) are notable opportunistic pathogens. As a result, microorganisms that often enter our households with water and are then enriched in novel indoor habitats might have a hitherto underestimated impact on the well-being of the increasingly indoor-bound human population. KEY POINTS: Domestic environment harbours a large diversity of microorganisms. Microbiota of water-related indoor habitats mainly originates from tap water. Bathrooms, kitchens and household appliances select for polyextremotolerant species. Many household-related microorganisms are human opportunistic pathogens.
Topics: Air Microbiology; Air Pollution, Indoor; Bacteria; Communicable Diseases; Disease Reservoirs; Drinking Water; Ecosystem; Fungi; Household Articles; Humans; Microbiota; RNA, Ribosomal, 16S; Temperature; Water Microbiology
PubMed: 32533304
DOI: 10.1007/s00253-020-10719-4 -
Journal of Leukocyte Biology Mar 2021xx
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Topics: Allergy and Immunology; COVID-19; History, 19th Century; History, 20th Century; Host-Pathogen Interactions; Humans; Macrophages; Microbiology; Microbiota; SARS-CoV-2
PubMed: 33630386
DOI: 10.1002/JLB.4CE0520-304RRR -
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 -
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 -
Microbiology (Reading, England) Jun 2024The past decade has seen growing awareness of the challenges faced by LGBTQIA+ scientists, including discrimination in the workplace and the lack of representation....
The past decade has seen growing awareness of the challenges faced by LGBTQIA+ scientists, including discrimination in the workplace and the lack of representation. Initiatives such as 500 Queer Scientists, Pride in STEM and the Microbiology Society's LGBTQIA+ events have been instrumental in promoting inclusivity in science, technology, engineering, mathematics and medicine (STEMM). The Microbiology Society and its members have played a pivotal role in these efforts and summarized here are their initiatives towards safer and more inclusive scientific and research environments. Starting with a series of interviews and blog posts about the experiences of LGBTQIA+ microbiologists in research, the Society has promoted the organization of networking and social events and developed guidelines for creating more inclusive scientific conferences. These initiatives have not only improved the representation and visibility of LGBTQIA+ individuals in microbiology, but have also served as a blueprint for similar efforts in other scientific areas. Nevertheless, despite improvements in some areas, full inclusion of LGBTQIA+ scientists is still hindered by societal and institutional policies around the world. Here, we propose novel measures to support and empower LGBTQIA+ microbiological communities within learned societies.
Topics: Humans; Sexual and Gender Minorities; Microbiology; Female; Male; Societies, Scientific
PubMed: 38860877
DOI: 10.1099/mic.0.001468 -
Journal of Bacteriology May 2024
Topics: Periodicals as Topic; Writing; Bacteriology
PubMed: 38624220
DOI: 10.1128/jb.00113-24 -
International Journal of Environmental... Sep 2022Soil microbial biomass (SMB) and soil microbial communities (SMCs) are the key factors in soil health and agricultural sustainability. We hypothesized that low...
Soil microbial biomass (SMB) and soil microbial communities (SMCs) are the key factors in soil health and agricultural sustainability. We hypothesized that low bioavailable carbon (C) and energy were the key limiting factors influencing soil microbial growth and developed a new fertilization system to address this: the simultaneous application of mineral fertilizers and high-energy-density organic amendments (HED-OAs). A microcosm soil incubation experiment and a subsp. pot culture experiment were used to test the effects of this new system. Compared to mineral fertilizer application alone, the simultaneous input of fertilizers and vegetable oil (SIFVO) achieved a bacterial abundance, fungal abundance, and fungal:bacterial ratio that were two orders of magnitude higher, significantly higher organic C and nitrogen (N) content, significantly lower N loss, and nearly net-zero NO emissions. We proposed an energy and nutrient threshold theory to explain the observed bacterial and fungal growth characteristics, challenging the previously established C:N ratio determination theory. Furthermore, SIFVO led to microbial community improvements (an increased fungal:bacterial ratio, enriched rhizosphere bacteria and fungi, and reduced N-transformation bacteria) that were beneficial for agricultural sustainability. A low vegetable oil rate (5 g/kg) significantly promoted subsp. growth and decreased the shoot N content by 35%, while a high rate caused severe N deficiency and significantly inhibited growth of the crop, confirming the exceptionally high microbial abundance and indicating severe microbe-crop competition for nutrients in the soil.
Topics: Bacteria; Carbon; Fertilizers; Nitrogen; Plant Oils; Soil; Soil Microbiology
PubMed: 36231512
DOI: 10.3390/ijerph191912212 -
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 -
The New Phytologist Jun 2022
Topics: Microbiota; Plant Roots; Plants; Rhizosphere; Soil Microbiology
PubMed: 35599439
DOI: 10.1111/nph.18187 -
The New Phytologist Mar 2023Feedbacks between plants and soil microbes form a keystone to terrestrial community and ecosystem dynamics. Recent advances in dissecting the spatial and temporal... (Review)
Review
Feedbacks between plants and soil microbes form a keystone to terrestrial community and ecosystem dynamics. Recent advances in dissecting the spatial and temporal dynamics of plant-soil feedbacks (PSFs) have challenged longstanding assumptions of spatially well-mixed microbial communities and exceedingly fast microbial assembly dynamics relative to plant lifespans. Instead, PSFs emerge from interactions that are inherently mismatched in spatial and temporal scales, and explicitly considering these spatial and temporal dynamics is crucial to understanding the contribution of PSFs to foundational ecological patterns. I propose a synthetic spatiotemporal framework for future research that pairs experimental and modeling approaches grounded in mechanism to improve predictability and generalizability of PSFs.
Topics: Ecosystem; Feedback; Soil; Plants; Soil Microbiology
PubMed: 36604846
DOI: 10.1111/nph.18719