-
Journal of Industrial Microbiology &... Apr 2022The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, nonfood... (Review)
Review
The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, nonfood carbohydrates, such as lignocellulosic biomass, can be used to produce next generation biofuels, including cellulosic ethanol and other nonethanol fuels like butanol. However, currently there is no native microorganism that can ferment all lignocellulosic sugars to fuel molecules. Thus, research is focused on engineering improved microbial biocatalysts for production of liquid fuels at high productivity, titer, and yield. A clear understanding and application of the basic principles of microbial physiology and biochemistry are crucial to achieve this goal. In this review, we present and discuss the construction of microbial biocatalysts that integrate these principles with ethanol-producing Escherichia coli as an example of metabolic engineering. These principles also apply to fermentation of lignocellulosic sugars to other chemicals that are currently produced from petroleum.
Topics: Biofuels; Biomass; Escherichia coli; Ethanol; Fermentation; Hexoses
PubMed: 33686428
DOI: 10.1093/jimb/kuab016 -
Genomics, Proteomics & Bioinformatics Feb 2015There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most... (Review)
Review
There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience.
Topics: Computational Biology; Databases, Factual; Humans; Internet; Microbiota
PubMed: 25721609
DOI: 10.1016/j.gpb.2015.01.008 -
Current Opinion in Microbiology Feb 2015RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are... (Review)
Review
RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are readily digitized and lend themselves to quantitative analysis. High-resolution RNA sequence (RNA-seq) data allows transcriptional features (promoters, terminators, operons, among others) to be pinpointed on any bacterial transcriptome. Once the transcriptome is mapped, the activity of transcriptional features can be quantified. Here we highlight how quantitative transcriptome analysis can reveal biological insights and briefly discuss some of the challenges to be faced by the field of bacterial transcriptomics in the near future.
Topics: Bacteria; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genetics, Microbial; High-Throughput Nucleotide Sequencing; Molecular Biology
PubMed: 25483350
DOI: 10.1016/j.mib.2014.11.011 -
Molecular Microbiology Mar 2020The acquisition process of antibiotic resistance in an otherwise susceptible organism is shaped by the ecology of the species. Unlike other relevant human pathogens,... (Review)
Review
The acquisition process of antibiotic resistance in an otherwise susceptible organism is shaped by the ecology of the species. Unlike other relevant human pathogens, Listeria monocytogenes has maintained a high rate of susceptibility to the antibiotics used for decades to treat human and animal infections. However, L. monocytogenes can acquire antibiotic resistance genes from other organisms' plasmids and conjugative transposons. Ecological factors could account for its susceptibility. L. monocytogenes is ubiquitous in nature, most frequently including reservoirs unexposed to antibiotics, including intracellular sanctuaries. L. monocytogenes has a remarkably closed genome, reflecting limited community interactions, small population sizes and high niche specialization. The L. monocytogenes species is divided into variants that are specialized in small specific niches, which reduces the possibility of coexistence with potential donors of antibiotic resistance. Interactions with potential donors are also hampered by interspecies antagonism. However, occasional increases in population sizes (and thus the possibility of acquiring antibiotic resistance) can derive from selection of the species based on intrinsic or acquired resistance to antibiotics, biocides, heavy metals or by a natural tolerance to extreme conditions. High-quality surveillance of the emergence of resistance to the key drugs used in primary therapy is mandatory.
Topics: Animals; Anti-Bacterial Agents; Bacterial Proteins; Drug Resistance, Bacterial; Drug Resistance, Microbial; Humans; Listeria monocytogenes; Microbial Sensitivity Tests; Plasmids
PubMed: 32185838
DOI: 10.1111/mmi.14454 -
Integrative and Comparative Biology Oct 2019The chemical ecology and chemical defenses of sponges have been investigated for decades; consequently, sponges are among the best understood marine organisms in terms... (Review)
Review
The chemical ecology and chemical defenses of sponges have been investigated for decades; consequently, sponges are among the best understood marine organisms in terms of their chemical ecology, from the level of molecules to ecosystems. Thousands of natural products have been isolated and characterized from sponges, and although relatively few of these compounds have been studied for their ecological functions, some are known to serve as chemical defenses against predators, microorganisms, fouling organisms, and other competitors. Sponges are hosts to an exceptional diversity of microorganisms, with almost 40 microbial phyla found in these associations to date. Microbial community composition and abundance are highly variable across host taxa, with a continuum from diverse assemblages of many microbial taxa to those that are dominated by a single microbial group. Microbial communities expand the nutritional repertoire of their hosts by providing access to inorganic and dissolved sources of nutrients. Not only does this continuum of microorganism-sponge associations lead to divergent nutritional characteristics in sponges, these associated microorganisms and symbionts have long been suspected, and are now known, to biosynthesize some of the natural products found in sponges. Modern "omics" tools provide ways to study these sponge-microbe associations that would have been difficult even a decade ago. Metabolomics facilitate comparisons of sponge compounds produced within and among taxa, and metagenomics and metatranscriptomics provide tools to understand the biology of host-microbe associations and the biosynthesis of ecologically relevant natural products. These combinations of ecological, microbiological, metabolomic and genomics tools, and techniques provide unprecedented opportunities to advance sponge biology and chemical ecology across many marine ecosystems.
Topics: Animals; Aquatic Organisms; Genome; Host Microbial Interactions; Microbiota; Porifera; Transcriptome
PubMed: 30942859
DOI: 10.1093/icb/icz014 -
Briefings in Bioinformatics Mar 2016In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a... (Review)
Review
In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.
Topics: Computational Biology; Fermentation; Food Contamination; Food Microbiology; Food Safety; Food Technology; Genetics, Microbial; Hazard Analysis and Critical Control Points; Microbiota
PubMed: 26082168
DOI: 10.1093/bib/bbv034 -
Current Opinion in Microbiology Aug 2017Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked... (Review)
Review
Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked the composition of these microbial communities with alterations in the host's health, behavior, and development, yet the causative mediators of host-microbiota interactions remain poorly understood. Advances in understanding and engineering these interactions require the development of genetic tools to probe the molecular interactions driving the structure and function of microbial communities as well as their interactions with their host. This review discusses the current challenges to rendering culturable, non-model members of microbial communities genetically tractable - including overcoming barriers to DNA delivery, achieving predictable gene expression, and applying CRISPR-based tools - and details recent efforts to create generalized pipelines that simplify and expedite the tool-development process. We use the bacteria present in the human gastrointestinal tract as representative microbiota to illustrate some of the recent achievements and future opportunities for genetic tool development.
Topics: Bacteria; Gastrointestinal Microbiome; Genetics, Microbial; Host-Pathogen Interactions; Humans; Molecular Biology; Symbiosis
PubMed: 28624690
DOI: 10.1016/j.mib.2017.05.006 -
Bioscience Trends Feb 2016Nosocomial infection is a kind of infection, which is spread in various hospital environments, and leads to many serious diseases (e.g. pneumonia, urinary tract... (Review)
Review
Nosocomial infection is a kind of infection, which is spread in various hospital environments, and leads to many serious diseases (e.g. pneumonia, urinary tract infection, gastroenteritis, and puerperal fever), and causes higher mortality than community-acquired infection. Bacteria are predominant among all the nosocomial infection-associated pathogens, thus a large number of antibiotics, such as aminoglycosides, penicillins, cephalosporins, and carbapenems, are adopted in clinical treatment. However, in recent years antibiotic resistance quickly spreads worldwide and causes a critical threat to public health. The predominant bacteria include Methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii. In these bacteria, resistance emerged from antibiotic resistant genes and many of those can be exchanged between bacteria. With technical advances, molecular mechanisms of resistance have been gradually unveiled. In this review, recent advances in knowledge about mechanisms by which (i) bacteria hydrolyze antibiotics (e.g. extended spectrum β-lactamases, (ii) AmpC β-lactamases, carbapenemases), (iii) avoid antibiotic targeting (e.g. mutated vanA and mecA genes), (iv) prevent antibiotic permeation (e.g. porin deficiency), or (v) excrete intracellular antibiotics (e.g. active efflux pump) are summarized.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Cross Infection; Drug Resistance, Microbial; Humans; Hydrolysis; Mutation; beta-Lactamases
PubMed: 26877142
DOI: 10.5582/bst.2016.01020 -
Environmental Microbiology Aug 2020Differential shotgun proteomics identifies proteins that discriminate between sets of samples based on differences in abundance. This methodology can be easily applied... (Review)
Review
Differential shotgun proteomics identifies proteins that discriminate between sets of samples based on differences in abundance. This methodology can be easily applied to study (i) specific microorganisms subjected to a variety of growth or stress conditions or (ii) different microorganisms sampled in the same condition. In microbiology, this comparison is particularly successful because differing microorganism phenotypes are explained by clearly altered abundances of key protein players. The extensive description and quantification of proteins from any given microorganism can be routinely obtained for several conditions within a few days by tandem mass spectrometry. Such protein-centred microbial molecular phenotyping is rich in information. However, well-designed experimental strategies, carefully parameterized analytical pipelines, and sound statistical approaches must be applied if the shotgun proteomic data are to be correctly interpreted. This minireview describes these key items for a quick molecular phenotyping based on label-free quantification shotgun proteomics.
Topics: Archaea; Bacteria; Fungi; Phenotype; Proteins; Proteomics; Tandem Mass Spectrometry
PubMed: 32133743
DOI: 10.1111/1462-2920.14975 -
Journal of Exposure Science &... Jan 2020The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built... (Review)
Review
The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Ecology; Gene Transfer, Horizontal; Humans
PubMed: 31591493
DOI: 10.1038/s41370-019-0171-0