-
Research in Microbiology Jun 2014
Topics: Gene Expression Regulation, Bacterial; Genetics, Microbial; History, 20th Century; Molecular Biology; Operon
PubMed: 24859146
DOI: 10.1016/j.resmic.2014.05.018 -
Research in Microbiology Dec 2007
Topics: Bacteria; Genetics, Microbial; Genome, Bacterial; Genomics
PubMed: 18082580
DOI: 10.1016/j.resmic.2007.10.003 -
Cell Sep 2015
Topics: Education, Graduate; Escherichia coli; Genetics, Microbial; History, 20th Century; Microbial Viability; New York
PubMed: 26359976
DOI: 10.1016/j.cell.2015.08.048 -
Microbiology Spectrum Aug 2014This article examines the role of genomics in the understanding and identification of O157:H7 enterohemorrhagic Escherichia coli (EHEC). We highlight the development of... (Review)
Review
This article examines the role of genomics in the understanding and identification of O157:H7 enterohemorrhagic Escherichia coli (EHEC). We highlight the development of novel molecular typing systems that are based on the genomic sequence that has been generated for this pathotype. The genomic comparisons of EHEC to other E. coli strains highlight the close relatedness of the O157 and O55 isolates and also identify other non-O157 clades of isolates that appear to have a different genomic history. Analysis within the EHEC isolates must be completed on a fine scale using whole-genome sequence-based approaches to assess both the conserved and lateral acquired gene content. The plethora of genomic data for EHEC isolates has provided the ability to examine this pathotype in detail, which has provided opportunities for novel surveillance, detection, and diagnostics.
Topics: Enterohemorrhagic Escherichia coli; Evolution, Molecular; Genetics, Microbial; Genome, Bacterial; Genomics; Microbiology; Molecular Typing
PubMed: 26104203
DOI: 10.1128/microbiolspec.EHEC-0020-2013 -
Beneficial Microbes Jun 2013Until recently, proper development of molecular studies in Bifidobacterium species has been hampered by growth difficulties, because of their exigent nutritive... (Review)
Review
Until recently, proper development of molecular studies in Bifidobacterium species has been hampered by growth difficulties, because of their exigent nutritive requirements, oxygen sensitivity and lack of efficient genetic tools. These studies, however, are critical to uncover the cross-talk between bifidobacteria and their hosts' cells and to prove unequivocally the supposed beneficial effects provided through the endogenous bifidobacterial populations or after ingestion as probiotics. The genome sequencing projects of different bifidobacterial strains have provided a wealth of genetic data that will be of much help in deciphering the molecular basis of the physiological properties of bifidobacteria. To this end, the purposeful development of stable cloning and expression vectors based on robust replicons - either from temperate phages or resident plasmids - is still needed. This review addresses the current knowledge on the mobile genetic elements of bifidobacteria (prophages, plasmids and transposons) and summarises the different types of vectors already available, together with the transformation procedures for introducing DNA into the cells. It also covers recent molecular studies performed with such vectors and incipient results on the genetic modification of these organisms, establishing the basis that would allow the use of bifidobacteria for future biotechnological applications.
Topics: Bifidobacterium; Gene Transfer Techniques; Genetic Engineering; Genetic Vectors; Genetics, Microbial; Humans; Interspersed Repetitive Sequences; Molecular Biology; Transformation, Bacterial
PubMed: 23271067
DOI: 10.3920/BM2012.0031 -
FEMS Microbiology Reviews Oct 1998
Topics: Genes; Genetics, Microbial
PubMed: 9862120
DOI: 10.1111/j.1574-6976.1998.tb00367.x -
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 -
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 -
Research in Microbiology Jun 2014
Topics: Gene Expression Regulation, Bacterial; Genetics, Microbial; History, 20th Century; Molecular Biology; Operon
PubMed: 24853970
DOI: 10.1016/j.resmic.2014.05.004