Microbiomics

Dimensions, Applications, and Translational Implications of Human and Environmental Microbiome Research

• Publisher: Academic Press
• Year: 2020
• ISBN:
  9780128172827
• Topic: Medicina
• Subtopic: Genetica in medicina

Microbiomics: Dimensions, Applications, and Translational Implications of Human and Environmental Microbiome Research describes a new, holistic approach to microbiomics. International experts provide in-depth discussion of current research methods for studying human, environmental, viral and fungal microbiomes, as well as the implications of new discoveries for human health, nutrition, disease, cancer research, probiotics and in the food and agricultural industries. Distinct chapters covering culturomics and sub-microbiomes, such as the viriome and mycetobiome, provide an integrative framework for the expansion of microbiomics into new areas of application, as well as crosspollination between research areas.

Detailed case studies include the use of microbiomics to develop natural products with antimicrobial properties, microbiomic enhancements in food and beverage technology, microbes for bioprotection and biopreservation, microbial tools to reduce antibiotic resistance, and maintenance and cultivation of human microbial communities.

• Provides an integrated approach for realizing the potential of microbiomics across the life, environmental, food and agricultural sciences
• Includes thorough analysis of human, environmental, viral and mycetol microbiomes, as well as methods and technology for identifying microbiotes
• Features chapter contributions from international leaders in microbiomic methods, technology and applications

Chapter 1

Introduction

The Microbiome as a Concept: Vogue or Necessity?

Manousos E. Kambouris¹ and Aristea Velegraki², ¹The Golden Helix Foundation, London, United Kingdom, ²Mycology Research Laboratory, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece

The notion of “microbiome” has no negative or threatening sound on principle. Both its standard and its projected forms (with a multitude of new microbiota) are applicable and important in bioindustry, bioremediation, biotechnology, in environmental applications, and perhaps even in energy. But the aspect of pathogenicity is undeniably the most important, and the one able to threaten our species with extinction. Thus this aspect is always preferentially studied in terms of resources of any kind.

The universe of OMICS is now a tridimensional one; the first, original dimension, coined before the turn of the millennium, referred to collectivities within a cell: genomics, proteomics, transcriptomics, metabolomics, interactomics, and their special subsets such as pharmaco/toxico/immunogenomics. The second dimension emerged in the late 2000s, and referred to collectivities or interactions of multiple cells or organisms. It was the time of infectiomics, microbiomics, and the different levels and categories of the latter. A third iteration appeared in the 2010s, centered on the methods of study and not the organisms or their constituents: metagenomics, radiomics, and culturomics.

The -ome/-omic sciences are really, at least in part, something of a vogue. The use of the suffixes has grown out of all proportion and necessity, to retouch sectors, make studies more relevant and projects more promising, even in cases that are accurately and correctly described by previous, pre-Omics terminology. But in Microbiology, the Microbiomic Culture is a true necessity, as it encompasses the multidimensional and holistic view of an integrative picture, where biotic (microbiota and macrobiota) and abiotic elements interact in multiple levels, which are digested in much deeper zoom than previously done by ecological studies through the concept of niches, cycles, and networks.

The concept of Microbiome is not entirely novel: the term contains the word “microbe” almost intact, with the suffix “-ome,” a latinicized version of the Greek suffix “-ωμα” denoting entirety, sum, or collectivity. Thus the Microbiome is the sum of all microbes sharing a common denominator, usually a common location/environment within a defined timeframe, as initially proposed in a largely forgotten stroke of foresight by Whipps et al. (1988), pg. 176: “A convenient ecological framework in which to examine biocontrol systems is that of the microbiome. This may be defined as a characteristic microbial community occupying a reasonably well defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity.”

There has been a tendency to use the term Microbiome to denote the sum of microbial genomes, as proposed by Hooper and Gordon (2001): “The Nobel laureate Joshua Lederberg has suggested using the term ‘microbiome’ to describe the collective genome of our indigenous microbes (microflora), the idea being that a comprehensive genetic view of Homo sapiens as a life-form should include the genes in our microbiome….” This context, apart from being hopelessly restrictive as it focuses solely in colonizing microbiota and, even worse, colonizers exclusively of Homo sapiens, and unimaginatively unidisciplinary, since it includes only a genetic/genomic aspect, is also both unclear, in its qualitative dimension, and inaccurate. Inaccurate, because there is not any letter in the word “microbiome” to attest to the genetic constituent of “genome,” as the suffix “-ome” is about collectivity and entirety. And unclear, as it does not unequivocally describe, even qualitatively, the entirety of microbial genomes, as it does not define the genomic unit within a taxon horizon: genomes of different subgenera and, even more prominently, of different subspecies is unclear whether they are scored as one or as multiple entities.

In its organism-centered use the term Microbiome supplants a very well-established concept, the microbial flora (Tancrede, 1992). The latter term denoted possible heterogeneity and a dynamic, multi-level structure expressed by multiple and different interactions, mainly with the “environment” but also among the different species and niches; the concept of “microbiome” though, infers to much higher, more diverse and more impactful interactions. In addition, it remedies the conceptual pitfall of flora, which by definition denotes kingdom Plantae, or, in a functional, food-chain aspect, photosynthetic organisms that can be expanded to include autotrophs/producers in general. On the contrary, many if not most members of microbial floras are heterotrophs (consumers and decomposers).

Another similar term has been the Microbial Community, denoting microbes coexisting in space and time (Escobar-Zepeda et al., 2015). The term and concept were quite handy, lacking only the pertaining notion of collectivity and conceptual unity needed to describe the constituting microbiota as one entity, differentiated from and possibly opposed to other entities participating actively in the definition of their environment or coexisting in the same spatiotemporal window. Furthermore, the unity or common denominator which defines a certain Microbiome does not have to be a 3D location, possibly augmented by a temporal dimension, although it usually is. But the microbiome might be a functional or other sum of microbial populations.

Moreover, “microbiome” pertains to two aspects previously underappreciated and not appropriately covered by the notion of “microbial flora.” The first such aspect is the motion of microbiota. Microbial flora echoes of motionlessness in spatial terms, while many microbiota are endowed with active motion/motility. Actually the concept of microbiome unifies both microbial flora and any functional concept of microbial fauna. Even in the lower microbiomatic levels, that is bacteriomes and viromes, the existence of actual predators or consumers, as are the predatory bacteria (Sockett, 2009) and the virophages (Bekliz et al., 2016; Katzourakis and Aswad, 2014), is analogous rather to faunal than to floral attributes and reminiscent of the more evolved, eukaryotic hyperparasites (Parratt and Laine, 2016).

The second aspect is that the microbial flora as a term and concept projects no notion whatsoever of the intense genetic processes inherent among microbiotes. The Plantae, which constitute the regular flora (or macroflora), are restricted to mispollination in this respect, with misfertilized plants producing sterile or dysfunctional fruit or ploidal variations. In stark contrast, microbiota, and especially Prokarya, present vigorous genetic mobility and exchange, a fact so prominent that the term “microbiome” is often erroneously used to denote the sum of genomes of the microbes, and not the microbiota proper, of a certain environment (Hooper and Gordon, 2001).

The concept of Microbiome is suitable for current and future needs to analyze and describe the explosive changes expected in microbiology due to biotechnology endeavors. It is the correct approach to investigate and comprehend intermingled and interacting microbial populations, as it does not imply the stable, dynamic but balanced condition of the microflora, where disturbances and changes are a diversion from the normality. The Microbiome may be understood as an instantaneous OR continuous entity, which incorporates the phenomena of nonlinear genetic exchange. It allows conceptual flexibility and room to accommodate (1) novel, engineered, or fully artificial microbiota (Hutchison et al., 2016; Smith et al., 2003; Malyshev et al., 2014), tentatively called “metapathogens” and “neopathogens” in their pathogenic capacities and depending on the degree of engineering (Kambouris et al., 2018); (2) the microbiota as appendages or symbiotic exo-organs of macroorganisms (Hooper and Goron, 2001), thus constituting (sub)microbiomes and individual microbiomes; (3) our expanded concept of microbiota, with the viruses being counted as proper lifeforms of acellular nature (Pearson, 2008) and an open door to extend such status to viroids; and (4) the genomic interactions implicating any nucleic acid form, from the single, possibly decaying DNA strands used in transformation to the elaborate mechanisms of transposition and transduction, which should be included, when in extracellular phase, in the “exogenome” (Kambouris et al., 2018).

The latter should be viewed as a collective, prospective pool of genetic information, which is potentially translatable depending on the receiver. The mind goes to prokaryotes, which incorporate any naked DNA by transformation, without any concern over its origin or sequence/meaning. Such randomly incorporated DNAs might introduce completely new protein threads, which may prime equal revolutionary events rather than evolutionary ones, by accumulating amino acid changes (individual or “en block”) in existing proteins or adding/eliminating protein families by transferable elements.

When considering eukaryotes, naked DNAs are used for catabolism and lateral transfer intercellularly is of questionable applicability. But transduction by viruses is another issue altogether. Gene disruption and specialized transduction are well-attested events, but insertion in an exomic sequence, especially if the viral function is inert (pseudovirus) or becomes so (either randomly or by cellular defense mechanisms), equally produces a totally novel protein. The event introduces within an open reading frame a sequence possibly read in a different one and definitely having different length and embedded regulation, and this holds true for both eukaryotic and prokaryotic host genomes.

The alleged “democratization” in different scientific and technological areas provides prospects but also hides dangers. The “self-crisping” (Ireland, 2017) of interested individuals toward therapy or deranged concepts of superpowers is an upsetting and even worrisome fact, mostly in social terms, but not alarming or unnerving. On the contrary, self-acclaimed microbiologists and biotechnologists may have tremendous biological, not social-only, impact. In future, in each block or neighborhood, a genomics-capable microbiological workshop, mostly illegitimate, may be run to produce amenities which today are covered by very different products (from drugs to food and weapons or powerful chemicals); it also may not. But the problem is that it DOES may happen. The inherent problems in research conduct, the current difficulty in performing second-generation sequencing, in terms of platform availability but also due to the exceptional needs in computational power (Escobar-Zepeda et al., 2015), might have been a safety feature, which will be removed by the oncoming third generation. Thus the methodological and cognitive tools to respond to a reality where the emergence of a new microbe happens many times a day in multiple, dispersed localities must be in place, even if this bleak prospect is considered improbable or unlikely. After all, the virtual humanity and the Internet of Things were considered scienceless fiction during the lifetime of today’s mainstay scientists.

References

1. Bekliz M, Colson P, La Scola B. The expanding family of virophages. Viruses. 2016;8(11):317–331.

2. Escobar-Zepeda A, Vera-Ponce de León A, Sanchez-Flores A. The road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics. Front Genet. 2015;6:348.

3. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science. 2001;292:1115–1118.

4. Hutchison CA, Chuang RY, Noskov VN, et al. Design and synthesis of a minimal bacterial genome. Science. 2016;351:6253.

5. Ireland, T., December 24, 2017. I want to help humans genetically modify themselves. The Guardian. Available from: <https://www.theguardian.com/science/2017/dec/24/josiah-zayner-diy-gene-editing-therapy-crispr-interview> (accessed 15.11.18.).

6. Kambouris ME, Gaitanis G, Manousopoulos Y, et al. Humanome versus microbiome: games of dominance and pan-biosurveillance in the Omics universe. OMICS-JIB. 2018;22(8):528–538.

7. Katzourakis A, Aswad A. The origins of giant viruses, viroph...