p.1
Mechanisms of Action of Probiotics
What mechanism do probiotics use to combat pathogens?
Competitive exclusion by blocking binding sites.
p.1
Mechanisms of Action of Probiotics
How do probiotics modulate the immune system?
By enhancing immune responses.
p.1
Clinical Applications of Probiotics
What are some clinical applications of probiotics mentioned?
Bacterial infections of the gastrointestinal tract and oral infections.
p.1
Microbiome in Fermented Foods
What is the focus of Chapter 12?
Microbiomic prospects in fermented food and beverage technology.
p.16
Microbiome Concept and Definitions
Why were viruses detached from the microbiome?
They possessed no consensus sequences.
p.17
Microbiome Concept and Definitions
What was the basis for the reclassification of Archaebacteria?
Stringent comparisons of rDNA sequences showed significant differences from other Prokarya.
p.15
Microbiome Concept and Definitions
What are the two approaches discussed in relation to metagenomics?
The shotgun approach and the consensus gene metagenomics.
p.9
Microbiome Concept and Definitions
What role do viruses play in the microbiome?
They are counted as proper lifeforms and can influence genomic interactions.
p.17
Microbiome Concept and Definitions
What factors were initially thought to influence the diversity of the human microbiome?
Illness, geographical locale, diet, lifestyle, age, and climate.
p.10
Microbiome Concept and Definitions
What is the role of hyperparasitism in microbial ecology?
It influences microbial pathogen ecology and evolution.
p.10
Microbiome Concept and Definitions
What is the relationship between human microflora and health?
Human microflora plays a crucial role in health and disease.
p.8
Microbiome Concept and Definitions
What criticism is made about the term 'Microbiome'?
It is seen as restrictive, unclear, and inaccurate, focusing only on genetic aspects.
p.2
Antimicrobial Treatments and History
What type of drugs are used to inhibit nucleic acids?
Nucleic acids inhibitors.
p.10
Microbiome Concept and Definitions
What is the significance of the emergence of new microbes?
It occurs many times a day in multiple, dispersed localities.
p.10
Microbiome Concept and Definitions
What are the current challenges in second-generation sequencing?
Platform availability and exceptional computational power needs.
p.10
Microbiome Concept and Definitions
How was the concept of virtual humanity and the Internet of Things perceived in the past?
They were considered science fiction during the lifetime of today's mainstay scientists.
p.10
Microbiome Concept and Definitions
What must be in place to respond to the emergence of new microbes?
Methodological and cognitive tools.
p.1
Microbiome in Fermented Foods
What types of products are discussed in relation to their microbiomes?
Naturally fermented dairy, meat, olives, pickles, wine, and beer.
p.15
Microbiome Concept and Definitions
What is viral transduction?
A process where viruses infect bacteria or archaea, allowing for interdomain transduction.
p.9
Microbiome Concept and Definitions
What does the microbiome concept imply about microbial populations?
It does not imply a stable condition but rather a dynamic and interacting entity.
p.17
Microbiome Concept and Definitions
What significant change was made to the classification of Archaebacteria?
They were reclassified as Archaea, a status higher than other taxa.
p.9
Microbiome Concept and Definitions
What is often erroneously denoted by the term 'microbiome'?
The sum of genomes of the microbes, rather than the microbiota proper.
p.8
Microbiome Concept and Definitions
What does the term 'Microbiome' encompass?
It refers to both the microorganisms involved and their theatre of activity.
p.17
Microbiome Concept and Definitions
What role does aging play in microbiomic diversity?
Aging contributes to diversity due to biochemical and microenvironmental changes.
p.7
Microbiome Concept and Definitions
What is the primary focus of microbiome studies?
The aspect of pathogenicity, which can threaten species with extinction.
p.9
Microbiome Concept and Definitions
How can prokaryotes incorporate naked DNA?
By transformation, without concern over its origin or sequence.
p.15
Microbiome Concept and Definitions
What is a significant drawback of consensus metagenomics?
It is conditional on the existence of universal consensus sequences; if they do not exist, the respective genomes are not analyzed.
p.12
Microbiome Concept and Definitions
What was the reaction of microbial geneticists to the term 'microbiome'?
They revived the term by giving it a genomic spin.
p.2
Electromagnetism and Microbiomes
What is the relationship between electromagnetism and microbiomes?
Electromagnetic fields can affect microbial behavior and interactions.
p.5
Microbiome Concept and Definitions
Where does Kristel Klaassen work?
Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
p.4
Microbiome Concept and Definitions
Where is Konstantinos Grivas affiliated?
Hellenic Military Academy, Kitsi, Greece.
p.6
Microbiome Concept and Definitions
Which university is associated with the culture collection mentioned?
National and Kapodistrian University of Athens.
p.9
Microbiome Concept and Definitions
How does the concept of microbiome accommodate novel or engineered microbiota?
It allows for flexibility to include metapathogens and neopathogens based on their pathogenic capacities.
p.3
Emerging Pathogens and Surveillance
What does the chapter suggest about the future of pathogen management?
It emphasizes projecting a responsive strategy and defining operational procedures.
p.12
Microbiome Concept and Definitions
What is a challenge in the use of the term 'bacteriome'?
Its scientific weight is not proportional to the studies conducted.
p.14
Microbiome Concept and Definitions
What is the significance of horizontal gene transfer (HGT) in prokaryotic organisms?
HGT allows the incorporation of novel genetic blueprints without procreation, leading to adaptation of recipient cells.
p.16
Microbiome Concept and Definitions
What is the significance of RNA viruses in the context of metatranscriptomics?
They allowed a reverse-transcriptase-primed procedure.
p.14
Microbiome Concept and Definitions
What complicates the definition of 'difference' in taxonomy among prokaryotes?
The presence of viruses and fungi, along with anamorphism and teleomorphism considerations.
p.16
Microbiome Concept and Definitions
What is the significance of the term 'archaeome'?
It distinguishes archaeal biomes from bacterial biomes.
p.5
Microbiome Concept and Definitions
Which laboratory is Yiannis N. Manoussopoulos associated with?
Laboratory of Virology, Plant Protection Division of Patras, ELGO-Demeter, NEO & Amerikis, Patras, Greece.
p.3
Microbiomics and Biosecurity
What is the focus of Chapter 15 in the document?
Microbiomics: A Focal Point in GCBR and Biosecurity.
p.17
Microbiome Concept and Definitions
What life stages are considered turning points that affect microbiomic diversity?
Birth, puberty, adulthood, and old age.
p.12
Microbiome Concept and Definitions
What is the focus of current studies in microbiome research?
The notion of bacteriome.
p.3
Emerging Pathogens and Surveillance
What does the chapter imply about the cognitive dimension in dealing with threats?
It suggests adapting our cognitive dimension to an evolving universe of threats.
p.13
Microbiome Concept and Definitions
How did the concept of microbiome evolve from the Human Genome Project?
It was structured on bacteria and aimed to address new problems in bioscience.
p.9
Microbiome Concept and Definitions
What potential risks are associated with democratization in scientific areas?
Illegitimate microbiological workshops could produce dangerous products, from drugs to weapons.
p.7
Microbiome Concept and Definitions
What does the suffix '-ome' signify in the term 'Microbiome'?
It denotes entirety, sum, or collectivity.
p.4
Microbiome Concept and Definitions
Which university is Patrı ´cia Pimentel de Barros affiliated with?
São Paulo State University (UNESP).
p.16
Microbiome Concept and Definitions
Why is the concept of domains in microbiology considered genomic?
Because it is based on the phylogenetic tree of life.
p.4
Microbiome Concept and Definitions
Which contributor is also associated with São Paulo State University?
Juliana Campos Junqueira.
p.6
Microbiome Concept and Definitions
Which department is Loukia Zerva associated with?
Department of Pathophysiology, School of Medicine.
p.3
Emerging Pathogens and Surveillance
What are the key themes discussed in Chapter 15?
Emergence of new pathogens, responsive strategies, surveillance, intervention, and threat assessment.
p.2
Antimicrobial Treatments and History
What are metabolic antagonists used for?
They are part of the current antibacterial arsenal.
p.9
Microbiome Concept and Definitions
What is the 'exogenome'?
A collective pool of genetic information potentially translatable depending on the receiver.
p.15
Microbiome Concept and Definitions
What was the goal of the Human Microbiome Project (HMP) and MetaHIT?
To discover the genes and (meta)genomes implicated in human physiology and the synthesis of metabolites.
p.12
Microbiome Concept and Definitions
When did the first returns of 'bacteriome' appear in PubMed titles?
Relatively early, in 1998.
p.14
Microbiome Concept and Definitions
What are the two defined biomes that coexist and interact in prokaryotes?
Bacteriome and archaeome.
p.14
Microbiome Concept and Definitions
What is the main difference between prokaryotic and eukaryotic evolutionary principles?
Prokaryotes use HGT to change genomic content, while eukaryotes reshuffle existing genes through recombination.
p.13
Microbiome Concept and Definitions
What does the output of metagenomic analysis consist of?
Metagenomes, which are genomic elements compiled from microbial sequences.
p.14
Microbiome Concept and Definitions
What is the relationship between gene conservation and taxonomic levels?
Gene conservation is inversely proportional to the order of the compared taxa.
p.5
Microbiome Concept and Definitions
What department does Chrysanthi Mitsagga belong to?
Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Nutrition, University of Thessaly, Karditsa, Greece.
p.5
Microbiome Concept and Definitions
What is the affiliation of Felipe de Camargo Ribeiro?
Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil.
p.6
Microbiome Concept and Definitions
What is the common affiliation of Maja Stojiljkovic and Branka Zukic?
Institute of Molecular Genetics and Genetic Engineering, University of Belgrade.
p.10
Microbiome Concept and Definitions
What does the term 'virophage' refer to?
A type of virus that suggests viruses are alive.
p.15
Microbiome Concept and Definitions
What is the main advantage of the consensus gene metagenomics approach?
It provides a qualitative list of biota, making it easier to compile sequences to metagenomes and annotate them to actual species.
p.13
Microbiome Concept and Definitions
What was the original use of the term 'bacteriome' in the late 1990s?
To describe a chimeric organ where bacterial symbionts resided within adapted host tissues.
p.7
Microbiome Concept and Definitions
What are the three dimensions of OMICS mentioned in the text?
1. Collectivities within a cell (genomics, proteomics, etc.), 2. Interactions of multiple cells or organisms (infectiomics, microbiomics), 3. Methods of study (metagenomics, radiomics, culturomics).
p.7
Microbiome Concept and Definitions
How does the text describe the term 'Microbiome'?
As the sum of all microbes sharing a common location/environment within a defined timeframe.
p.15
Microbiome Concept and Definitions
What is the recommended approach for metagenomic analysis?
A combination of both shotgun and consensus gene metagenomics.
p.7
Microbiome Concept and Definitions
Why is the Microbiomic Culture considered a necessity in microbiology?
It provides a multidimensional and holistic view of interactions between biotic and abiotic elements.
p.13
Microbiome Concept and Definitions
Why is the genomic dimension of the human microbiome considered grandiose?
Due to the astounding number of microbial cells and genes, comparable to the human genome.
p.5
Microbiome Concept and Definitions
Where does Eleftherios Mylonakis work?
Infectious Diseases Division, Alpert Medical School & Brown University, Providence, RI, United States.
p.5
Microbiome Concept and Definitions
Where does Rodnei Dennis Rossoni work?
Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos, São Paulo, Brazil.
p.17
Microbiome Concept and Definitions
How can microbiota differ within the same individual?
Different body sites (bio-compartments) may be colonized by dissimilar microbiota.
p.1
Microbiome in Fermented Foods
What is a key aspect of the microbiome of naturally fermented dairy products?
Resolving the composition of the microbiomes.
p.3
Emerging Pathogens and Surveillance
What is the significance of surveillance in the context of Chapter 15?
Surveillance is crucial for vigilance against emerging pathogens.
p.8
Microbiome Concept and Definitions
What does the suffix '-ome' imply in the term 'Microbiome'?
It implies collectivity and entirety, not specifically genetic constituents.
p.8
Microbiome Concept and Definitions
How does the concept of 'Microbial Flora' differ from 'Microbiome'?
'Microbial Flora' denotes heterogeneity and dynamic interactions, while 'Microbiome' suggests higher, more diverse interactions.
p.3
Emerging Pathogens and Surveillance
What is the concluding question posed in Chapter 15?
Is it a dream or a nightmare?
p.9
Microbiome Concept and Definitions
What is the significance of gene disruption and specialized transduction?
They can introduce novel proteins into host genomes, affecting both eukaryotic and prokaryotic organisms.
p.8
Microbiome Concept and Definitions
What are the two aspects of microbiomes that were previously underappreciated?
The motion of microbiota and the intense genetic processes among them.
p.5
Microbiome Concept and Definitions
What is the affiliation of Maria Kantzanou?
Department of Hygiene, Epidemiology & Medical Statistics, National Retrovirus Reference Center, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
p.5
Microbiome Concept and Definitions
What is Martin Laurence's affiliation?
Shipshaw Labs, Montreal, QC, Canada.
p.4
Microbiome Concept and Definitions
What organization is Manousos E. Kambouris part of?
The Golden Helix Foundation, London.
p.8
Microbiome Concept and Definitions
How has the term 'Microbiome' been used in relation to microbial genomes?
It has been used to denote the sum of microbial genomes, focusing solely on colonizing microbiota.
p.15
Microbiome Concept and Definitions
What challenge does the shotgun approach face?
It can produce a lot of sequence noise, making it difficult to identify and quantify species/taxa in a sample.
p.12
Microbiome Concept and Definitions
What does the term 'microbiome' imply?
The collectivity of microbes in a spatiotemporal entity.
p.14
Microbiome Concept and Definitions
How does gene transfer affect phylogeny and identification in prokaryotic organisms?
It actively changes genomic content, complicating phylogenetic relationships and identification.
p.4
Microbiome Concept and Definitions
Where does Ilias Boltsis work?
Erasmus Medical Centre, Rotterdam, The Netherlands.
p.4
Microbiome Concept and Definitions
Which laboratory is Paraskevi Bouki associated with?
Laboratory of Food Microbiology and Biotechnology.
p.7
Microbiome Concept and Definitions
What was the original proposal regarding the microbiome made by Whipps et al. in 1988?
It was defined as a characteristic microbial community occupying a reasonably well-defined habitat.
p.4
Microbiome Concept and Definitions
What is Georgios Gaitanis's area of expertise?
Department of Skin and Venereal Diseases.
p.4
Microbiome Concept and Definitions
What department does Dimitris Glistras belong to?
Department of History and Archaeology, National and Kapodistrian University of Athens.
p.2
Antibiotic Resistance Strategies
What are efflux pump inhibitors used for?
To combat antibiotic resistance.
p.8
Microbiome Concept and Definitions
What is a key aspect of the term 'Microbiome' that is not covered by 'Microbial Flora'?
The motion of microbiota, as many are motile, unlike the static notion of flora.
p.8
Microbiome Concept and Definitions
What does the term 'Microbial Community' refer to?
It denotes microbes coexisting in space and time.
p.4
Microbiome Concept and Definitions
What department is Constantinos A. Chassomeris part of?
Department of Pharmacy, University of Patras.
p.7
Microbiome Concept and Definitions
What industries can benefit from the concept of microbiome?
Bioindustry, bioremediation, biotechnology, environmental applications, and energy.
p.16
Microbiome Concept and Definitions
What is the general trend regarding the recognition of bacteriome and archaeome?
There is widespread reluctance to recognize or refer to them.
p.5
Microbiome Concept and Definitions
What are the affiliations of George P. Patrinos?
Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece; Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, United Arabic Emirates; Faculty of Medicine and Health Sciences, Department of Pathology, Bioinformatics Unit, Erasmus University Medical Center, Rotterdam, The Netherlands.
p.3
Emerging Pathogens and Surveillance
What is the purpose of compiling a threat library as mentioned in Chapter 15?
To assess and understand the traits of emerging threats.
p.13
Microbiome Concept and Definitions
What challenge did researchers face when sequencing additional organisms beyond humans?
Issues of choice and processing of respective samples requiring different handling principles.
p.13
Microbiome Concept and Definitions
What is metagenomics?
A genomic approach to map the diversity of microbial genes encountered in the human body.
p.2
Antibiotic Resistance Strategies
What are beta-lactamase inhibitors used for?
To inhibit enzymes that confer resistance to beta-lactam antibiotics.
p.14
Microbiome Concept and Definitions
What are some proprietary processes of DNA exchange in Archaea?
DNA exchange through vesicles and cell fusion.
p.4
Microbiome Concept and Definitions
Where does Rose Ghemrawi work?
College of Pharmacy, Al Ain University, Abu Dhabi.
p.5
Microbiome Concept and Definitions
What department is Basilis Papathanasiou part of?
Department of Turkish and Contemporary Asian Studies, National and Kapodistrian University of Athens, Athens, Greece.
p.2
Antimicrobial Treatments and History
What is the focus of new approaches in antimicrobial discovery?
Innovative strategies to combat resistance and discover new drugs.
p.2
Antimicrobial Treatments and History
What is the significance of the two-component system in antimicrobial intervention?
It plays a role in bacterial response to environmental changes.
p.16
Microbiome Concept and Definitions
What is the cell number of fungi compared to prokarya?
Fungi make up a fraction of that of prokarya, approximately 0.1%.
p.13
Microbiome Concept and Definitions
What issue arises from counting microbial genes in a population?
The estimates refer to gene types, not actual genes, leading to potential discrepancies.
p.5
Microbiome Concept and Definitions
Where does Sonja Pavlovic work?
Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
