-
FEMS Microbiology Letters Aug 2019In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned... (Review)
Review
In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology is presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28 654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multi-scale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of 'more microbiology' is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.
Topics: Artificial Intelligence; Meta-Analysis as Topic; Microbiology; Publications; Software; Systems Biology
PubMed: 31314103
DOI: 10.1093/femsle/fnz159 -
MBio May 2017The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to...
The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to understand how microbes sustain myriad biochemical processes that maintain Earth. With this explosion in scientific output, a significant bottleneck has been the ability to rapidly disseminate new knowledge to peers and the public. Preprints have emerged as a tool that a growing number of microbiologists are using to overcome this bottleneck. Posting preprints can help to transparently recruit a more diverse pool of reviewers prior to submitting to a journal for formal peer review. Although the use of preprints is still limited in the biological sciences, early indications are that preprints are a robust tool that can complement and enhance peer-reviewed publications. As publishing moves to embrace advances in Internet technology, there are many opportunities for preprints and peer-reviewed journals to coexist in the same ecosystem.
Topics: Information Dissemination; Microbiology; Publishing
PubMed: 28536284
DOI: 10.1128/mBio.00438-17 -
Brazilian Journal of Microbiology :... Dec 2016Fresh produce is a generalized term for a group of farm-produced crops, including fruits and vegetables. Organic agriculture has been on the rise and attracting the... (Review)
Review
Fresh produce is a generalized term for a group of farm-produced crops, including fruits and vegetables. Organic agriculture has been on the rise and attracting the attention of the food production sector, since it uses eco-agricultural principles that are ostensibly environmentally-friendly and provides products potentially free from the residues of agrochemicals. Organic farming practices such as the use of animal manure can however increase the risk of contamination by enteric pathogenic microorganisms and may consequently pose health risks. A number of scientific studies conducted in different countries have compared the microbiological quality of produce samples from organic and conventional production and results are contradictory. While some have reported greater microbial counts in fresh produce from organic production, other studies do not. This manuscript provides a brief review of the current knowledge and summarizes data on the occurrence of pathogenic microorganisms in vegetables from organic production.
Topics: Animals; Food Contamination; Food Microbiology; Foodborne Diseases; Humans; Microbiology; Organic Agriculture
PubMed: 27825766
DOI: 10.1016/j.bjm.2016.10.006 -
Environmental Microbiology Oct 2019The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of... (Review)
Review
The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy ( ) define the direction and energy yield of a reaction; they do not. is one part of the actual Gibbs energy of a reaction (ΔG ), with a second part accounting for deviations from the standard composition. It is also frequently assumed that applies only to 25 °C and 1 bar; it does not. is a function of temperature and pressure. Here, we review how to determine ΔG as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔG and highlighting the large effects when multi-valent ions are part of the reaction. We also calculate ΔG for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.
Topics: Bacteria; Ecosystem; Energy Metabolism; Environmental Microbiology; Geologic Sediments; Water Microbiology
PubMed: 31403238
DOI: 10.1111/1462-2920.14778 -
FEMS Microbiology Reviews Nov 2020Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so... (Review)
Review
Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selective pressures and physicochemical constraints? If so, a broadly-applicable theory might be developed that predicts common microbiological behaviours. Microbial systems biologists have been working out the contours of this theory for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, metabolism, cell composition and steady-state growth. The theory makes predictions about fitness costs and benefits of protein expression, physicochemical constraints on cell growth and characteristics of optimal metabolisms that maximise growth rate. Comparisons of the theory with experimental data indicates that microorganisms often aim for maximisation of growth rate, also in the presence of stresses; they often express optimal metabolisms and metabolic proteins at optimal concentrations. This review explains the current status of the theory for microbiologists; its roots, predictions, experimental evidence and future directions.
Topics: Bacteria; Bacterial Physiological Phenomena; Microbiology; Systems Biology
PubMed: 33099619
DOI: 10.1093/femsre/fuaa034 -
Nihon Saikingaku Zasshi. Japanese... 2018
Topics: Animals; Bacteria; Bacterial Infections; Bacteriology; Fungi; Genome, Bacterial; Humans; Microbiology; Societies, Scientific
PubMed: 29479024
DOI: 10.3412/jsb.73.50 -
PLoS Biology Aug 2018In the context of biology as a whole and of our own personal lives, seemingly small things can prove surprisingly influential. Here, I consider the powerful impact of...
In the context of biology as a whole and of our own personal lives, seemingly small things can prove surprisingly influential. Here, I consider the powerful impact of small organisms-the inhabitants of the microbial world-and the small events that shaped my own development as a scientist. I reflect on the early days of the fields of molecular biology and microbial ecology and my own role in the origin story of what we now call "metagenomics".
Topics: Bacteria; Humans; Metagenomics; Microbiology
PubMed: 30142153
DOI: 10.1371/journal.pbio.3000009 -
Future Microbiology Jun 2021This interview was conducted by Atiya Henry, Commissioning Editor of . Joseph M Blondeau, MSc, PhD, RSM(CCM), SM(AAM), SM(ASCP), FCCP is a Clinical Microbiologist and...
This interview was conducted by Atiya Henry, Commissioning Editor of . Joseph M Blondeau, MSc, PhD, RSM(CCM), SM(AAM), SM(ASCP), FCCP is a Clinical Microbiologist and Head of Clinical Microbiology at Royal University Hospital (Saskatoon Health Region) and the University of Saskatchewan in Saskatoon, Canada. He is also the Provincial Clinical Lead for Microbiology in Saskatchewan, Canada. He holds a Masters of Sciences in Microbiology from Dalhousie University (1985) and a Doctor of Philosophy in Medical Microbiology from the University of Manitoba (1989). Following completion of his PhD, he completed an 1-month post-doctoral training in an infectious diseases research laboratory at Dalhousie University and following which he completed a 2-year post-doctoral residency training program in Clinical Microbiology, also at Dalhousie University. He holds appointments as a Clinical Associate Professor of Pathology, Adjunct Professor of Microbiology and Immunology and Clinical Associate Professor of Ophthalmology. He teaches to undergraduate and graduate students in the areas of microbiology, infectious diseases, antimicrobial agents and pharmacology. Dr Blondeau's main research interests are in the area of antimicrobial agents and antimicrobial resistance, clinical microbiology and clinical outcomes associated with antimicrobial therapy in both human and veterinary medicine.
Topics: COVID-19; Clinical Medicine; Forecasting; History, 20th Century; History, 21st Century; Humans; Laboratories; Microbiology
PubMed: 34082568
DOI: 10.2217/fmb-2021-0113 -
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 -
Poultry Science Sep 2011Eggs from alternative production practices are a growing niche in the market. Meeting consumer requests for greater diversity in retail egg options has resulted in some...
Eggs from alternative production practices are a growing niche in the market. Meeting consumer requests for greater diversity in retail egg options has resulted in some unique challenges such as understanding the food safety implications of eggs from alternative production practices. A study was conducted to determine what, if any, differences exist between nest run conventional cage-produced eggs and free range-produced eggs. A sister flock of brown egg layers was maintained in conventional cage and free-range production with egg and environmental sampling every 6 wk from 20 to 79 wk of age. Aerobic, coliform, and yeast and mold populations were monitored. Environmental microbial levels were not always indicative of egg contamination levels. When significant differences (P < 0.05 and P < 0.0001, dependent on season) were observed among treatments for coliforms, shell contamination levels of free-range nest box eggs and free-range floor eggs were always greater than those of conventional cage eggs, which remained low throughout the study (0.42-0.02 log cfu/mL). Shell yeast and mold levels were significantly greater in free-range floor eggs than in free-range nest box eggs and conventional cage eggs throughout the entire study. Egg contents contamination levels were extremely low for all monitored populations and treatments. Season of the year played a role in both environmental and egg microbial levels. Winter had the lowest levels of all populations monitored for all treatments, except for aerobic free-range floor egg shell emulsions, which were increased (3.6 log cfu/mL). Understanding the differences in microbial populations present on conventional cage-produced and free range-produced eggs can lead to the development of effective cleaning procedures, enhancing food safety.
Topics: Animal Husbandry; Animals; Chickens; Environmental Microbiology; Female; Food Microbiology; Oviposition; Ovum; Seasons
PubMed: 21844274
DOI: 10.3382/ps.2010-01139