Microbiome
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A microbiome (from
The
All animals and plants form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and the multi-member microbiome. The potential for microbiomes to influence the health, physiology, behaviour, and ecology of marine animals could alter current understandings of how marine animals adapt to change. This applies to especially the growing climate-related and anthropogenic-induced changes already impacting the ocean. The
Microbiome research originated in microbiology back in the seventeenth century. The development of new techniques and equipment boosted microbiological research and caused paradigm shifts in understanding health and disease.
Background
History
Microbiome research originated in microbiology and started back in the seventeenth century. The development of new techniques and equipment has boosted microbiological research and caused paradigm shifts in understanding health and disease. Since infectious diseases have affected human populations throughout most of history, medical microbiology was the earliest focus of research and public interest. Additionally, food microbiology is an old field of empirical applications. The development of the first microscopes allowed the discovery of a new, unknown world and led to the identification of microorganisms.[2]
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Shift of paradigm from microbes as unsocial organisms causing diseases to a holistic view of microorganisms as the centre of theOne Health Concept interconnecting all areas of human lives.[2]
Access to the previously invisible world opened the eyes and the minds of the researchers of the seventeenth century.
However, comprehensive research over the past century has shown only a small proportion of microorganisms are associated with disease or pathogenicity. The overwhelming majority of
Subsequently, the concept that microorganisms exist as single cells began to change as it became increasingly obvious that microbes occur within complex assemblages in which species interactions and communication are critical to population dynamics and functional activities.
A further important step was the introduction of
Another major paradigm shift was initiated at the beginning of this century and continues through today, as new sequencing technologies and accumulated sequence data have highlighted both the ubiquity of
Etymology
The word microbiome (from the Greek micro meaning "small" and bíos meaning "life") was first used by J.L. Mohr in 1952 in The Scientific Monthly to mean the microorganisms found in a specific environment.[59][60]
Definitions
Microbial communities have commonly been defined as the collection of microorganisms living together. More specifically, microbial communities are defined as multi-species assemblages, in which (micro) organisms interact with each other in a contiguous environment.[61] In 1988, Whipps and colleagues working on the ecology of rhizosphere microorganisms provided the first definition of the term microbiome.[62] They described the microbiome as a combination of the words micro and biome, naming a "characteristic microbial community" in a "reasonably well-defined habitat which has distinct physio-chemical properties" as their "theatre of activity". This definition represents a substantial advancement of the definition of a microbial community, as it defines a microbial community with distinct properties and functions and its interactions with its environment, resulting in the formation of specific ecological niches.[2]
However, many other microbiome definitions have been published in recent decades. By 2020 the most cited definition was by
Microbiome definitions[2] | |
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Definition type | Examples |
Ecological | Definitions based on ecology describe the microbiome following the concepts derived from the ecology of multicellular organisms. The main issue here is that the theories from the macro-ecology do not always fit the rules in the microbial world. |
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Organisms/host-dependent | The host-dependent definitions are based on the microbial interactions with the host. The main gaps here concern the question whether the microbial-host interaction data gained from one host can be transferred to another. The understanding of coevolution and selection in the host-dependent definitions is also underrepresented. |
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Genomic/ method-driven | There is a variety of microbiome definitions available that are driven by the methods applied. Mostly, these definitions rely on DNA sequence-based analysis and describe microbiome as a collective genome of microorganisms in a specific environment. The main bottleneck here is that every new available technology will result in a need for a new definition. |
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Combined | There are some microbiome definitions available that fit several categories with their advantages and disadvantages. |
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In 2020, a panel of international experts, organised by the EU-funded MicrobiomeSupport project,[76] published the results of their deliberations on the definition of the microbiome.[2] The panel was composed of about 40 leaders from diverse microbiome areas, and about one hundred further experts from around the world contributed through an online survey. They proposed a definition of the microbiome based on a revival of what they characterised as the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al. in 1988,[62] amended with a set of recommendations considering subsequent technological developments and research findings. They clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome.[2]
The panel extended the Whipps et al. definition, which contains all important points that are valid even 30 years after its publication in 1988, by two explanatory paragraphs differentiating the terms microbiome and microbiota and pronouncing its dynamic character, as follows:
- The microbiome is defined as a characteristic microbial community occupying a reasonable well-defined habitat which has distinct physio-chemical properties. The microbiome not only refers to the microorganisms involved but also encompass their theatre of activity, which results in the formation of specific ecological niches. The microbiome, which forms a dynamic and interactive micro-ecosystem prone to change in time and scale, is integrated in macro-ecosystems including eukaryotic hosts, and here crucial for their functioning and health.[2]
- The microbiota consists of the assembly of microorganisms belonging to different kingdoms (prokaryotes (bacteria, archaea), eukaryotes (algae, protozoa, fungi etc), while "their theatre of activity" includes microbial structures, metabolites, mobile genetic elements (such as transposons, phages, and viruses), and relic DNA embedded in the environmental conditions of the habitat.[2]
Membership
Microbiota
The microbiota comprises all living members forming the microbiome. Most microbiome researchers agree bacteria, archaea, fungi, algae, and small protists should be considered as members of the microbiome.
When it comes to the use of specific terms, a clear differentiation between microbiome and microbiota helps to avoid the controversy concerning the members of a microbiome.[2] Microbiota is usually defined as the assemblage of living microorganisms present in a defined environment.[64] As phages, viruses, plasmids, prions, viroids, and free DNA are usually not considered as living microorganisms,[80] they do not belong to the microbiota.[2]
The term microbiome, as it was originally postulated by Whipps and coworkers,
Microbiome studies sometimes focus on the behaviour of a specific group of microbiota, generally in relation to or justified by a clear hypothesis. More and more terms like
Networks
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Co-occurrence networks help visualising microbial interactions
Nodes usually represent taxa of microorganisms, and edges represent statistically significant associations between nodes.[2]
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Testing of the hypotheses resulted from the network analyses is required for a comprehensive study of microbial interactions.[2]
Microbes interact with one another, and these symbiotic interactions have diverse consequences for microbial fitness, population dynamics, and functional capacities within the microbiome.
Microbiomes exhibit different adaptive strategies.[2] Oligotrophs are organisms that can live in an environment offering very low levels of nutrients, particularly carbon. They are characterised by slow growth, low rates of metabolism, and generally low population density. Oligotrophic environments include deep oceanic sediments, caves, glacial and polar ice, deep subsurface soil, aquifers, ocean waters, and leached soils. In contrast are the copiotrophs, which thrive in much higher carbon concentrations, and do well in high organic substrate conditions such as sewage lagoons.[85][86]
In addition to oligotrophic and copiotrophic strategists, the
Coevolution
-
from "separation" theories to a holistic approachIn a holistic approach, the hosts and their associated microbiota are assumed to have coevolved with each other [2]
According to the "separation" approach, the microorganisms can be divided into pathogens, neutral, and symbionts, depending on their interaction with their host. The coevolution between host and its associated microbiota may be accordingly described as antagonistic (based on negative interactions) or mutualistic (based on positive interactions).[2][89]
As of 2020, the emergence in publications about
Types
Marine
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Relationships are generally thought to exist in a symbiotic state, and are normally exposed to environmental and animal-specific factors that may cause natural variations. Some events may change the relationship into a functioning but altered symbiotic state, whereas extreme stress events may cause dysbiosis or a breakdown of the relationship and interactions.[90]
All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment.[90]
The microbiomes of diverse marine animals are currently under study, from simplistic organisms including sponges[91] and ctenophores [92] to more complex organisms such as sea squirts[93] and sharks.[94][90]
The relationship between the
The gutless marine
Sponges are common members of the ocean's diverse benthic habitats and their abundance and ability to filter large volumes of seawater have led to the awareness that these organisms play critical roles in influencing benthic and pelagic processes in the ocean.[109] They are one of the oldest lineages of animals, and have a relatively simple body plan that commonly associates with bacteria, archaea, algal protists, fungi, and viruses.[110] Sponge microbiomes are composed of specialists and generalists, and complexity of their microbiome appears to be shaped by host phylogeny.[111] Studies have shown that the sponge microbiome contributes to nitrogen cycling in the oceans, especially through the oxidation of ammonia by archaea and bacteria.[112][113] Most recently, microbial symbionts of tropical sponges were shown to produce and store polyphosphate granules,[114] perhaps enabling the host to survive periods of phosphate depletion in oligotrophic marine environments.[115] The microbiomes of some sponge species do appear to change in community structure in response to changing environmental conditions, including temperature[116] and ocean acidification,[117][118] as well as synergistic impacts.[119]
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Collecting a sample of blow from a blue whale using a helicopter drone [120]
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Relative abundance of bacterial classes from whale blow, air and seawater samples.[121]
Terrestrial
Plant
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Microbiomes in the plant ecosystem [127]
The
Plant microbiomes are shaped by both factors related to the plant itself, such as genotype, organ, species and health status, as well as factors related to the plant's environment, such as management, land use and climate.[132] The health status of a plant has been reported in some studies to be reflected by or linked to its microbiome.[133][128][134][129]
Plant and plant-associated microbiota colonise different niches on and inside the plant tissue. All the above-ground plant parts together, called the phyllosphere, are a continuously evolving habitat due to ultraviolet (UV) radiation and altering climatic conditions. It is primarily composed of leaves. Below-ground plant parts, mainly roots, are generally influenced by soil properties. Harmful interactions affect the plant growth through pathogenic activities of some microbiota members. On the other hand, beneficial microbial interactions promote plant growth.[127]
Animal
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Principal coordinate analysis of animal gut microbiome data [135]
The mammalian gut microbiome has emerged as a key regulator of host
The importance of phylogeny-correlated factors to the diversity of vertebrate microbiomes more generally is still poorly understood.
Without broader evolutionary context, it is unclear how universally conserved patterns of host-microbe phylosymbiosis actually are. Growing evidence indicates that the strong patterns identified in mammals are the exception rather than the rule in vertebrates.
Human
The
Humans are colonised by many microorganisms, with approximately the same order of magnitude of non-human cells as human cells.
The Human Microbiome Project (HMP) took on the project of sequencing the genome of the human microbiota, focusing particularly on the microbiota that normally inhabit the skin, mouth, nose, digestive tract, and vagina.[155] It reached a milestone in 2012 when it published its initial results.[160]
Assessment
Currently available methods for studying microbiomes, so-called
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Methods for assessing microbial functioningComplex microbiome studies cover various areas, starting from the level of complete microbial cells (single cell genomics, metabarcoding, metagenomics), RNA (metatranscriptomics), protein (metaproteomics), and metabolites (metabolomics). In that order, the focus of the studies shifts from the microbial potential (learning about available microbiota in the given habitat) over the metabolic potential (deciphering available genetic material) towards microbial functioning (e.g., the discovery of the active metabolic pathways).[2]
As of 2020, understanding remains limited due to missing links between the massive availability of microbiome
The number of prokaryotic phyla may reach hundreds, and archaeal ones are among the least studied.
Each microbiome system is suited to address different types of questions based on the culturability of microbes, genetic tractability of microbes and host (where relevant), ability to maintain system in laboratory setting, and ability to make host/environment germfree.[172]
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Tradeoffs between experimental questions and complexity of microbiome systemsgnotobiotic mice is crucial for making links between host diet and the effects on specific microbial taxa in a community.[172]
See also
- Earth Microbiome Project
- Human microbiome
- Initial acquisition of microbiota
- Microbial population biology
- Microbiomes of the built environment
- Mycobiome
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Microbiome
This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. This definition is based on that of "biome," the biotic and abiotic factors of given environments. Others in the field limit the definition of microbiome to the collection of genes and genomes of members of a microbiota. It is argued that this is the definition of metagenome - ^ OCLC 886600661.
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we review literature on trimethylamine (TMA), a microbiota-generated metabolite linked to atherosclerosis development.
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Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form.
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