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122-453: A microbiome (from Ancient Greek μικρός (mikrós)  'small' and βίος (bíos)  'life') is the community of microorganisms that can usually be found living together in any given habitat . It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to

244-408: A cetacean 's gut microbiome. The most common is collecting fecal samples from the environment and taking a probe from the center that is non-contaminated. The skin is a barrier protecting marine mammals from the outside world. The epidermal microbiome on the skin is an indicator of how healthy the animal is, and is also an ecological indicator of the state of the surrounding environment. Knowing what

366-537: A pitch accent . In Modern Greek, all vowels and consonants are short. Many vowels and diphthongs once pronounced distinctly are pronounced as /i/ ( iotacism ). Some of the stops and glides in diphthongs have become fricatives , and the pitch accent has changed to a stress accent . Many of the changes took place in the Koine Greek period. The writing system of Modern Greek, however, does not reflect all pronunciation changes. The examples below represent Attic Greek in

488-404: A body space or other environment. Marchesi and Ravel focused in their definition on the genomes and microbial (and viral) gene expression patterns and proteomes in a given environment and its prevailing biotic and abiotic conditions. All these definitions imply that general concepts of macro-ecology could be easily applied to microbe-microbe as well as to microbe-host interactions. However,

610-415: A broader analysis of habitats with the highest proportion of 80% in some samples. Despite its omnipresence and abundance, relic DNA had a minimal effect on estimates of taxonomic and phylogenetic diversity. 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. Microbiota is usually defined as

732-448: A challenge to understanding prokaryotic functional diversity . The number of prokaryotic phyla may reach hundreds, and archaeal ones are among the least studied. The growing gap between the diversity of Bacteria and Archaea held in pure culture and those detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet cultured taxa, primarily based on sequence information. According to this proposal,

854-436: A community and use a mathematical modeling strategy such as flux balance analysis to predict the metabolic function of the microbial community at a taxon and community-level. As of 2020, understanding remains limited due to missing links between the massive availability of microbiome DNA sequence data on the one hand and limited availability of microbial isolates needed to confirm metagenomic predictions of gene function on

976-415: A diverse range of microbial species, and are adjustable to serve a variety of industrial and ecological interests. For synthetic biology , consortia take the ability to engineer novel cell behaviors to a population level. Consortia are more common than not in nature, and generally prove to be more robust than monocultures. Just over 7,000 species of bacteria have been cultured and identified to date. Many of

1098-434: A few taxa at a time, and variable methods for both surveying the microbiome and measuring phylosymbiosis and host specificity (or the restriction of microbes to specific host lineages) have made generalisations difficult. 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

1220-482: A first indication of microorganisms interacting within complex communities . Robert Koch 's explanation of the origin of human and animal diseases as a consequence of microbial infection and development of the concept of pathogenicity was an important milestone in microbiology. These findings shifted the focus of the research community and the public on the role of microorganisms as disease-forming agents that needed to be eliminated. However, comprehensive research over

1342-405: A high xylanase activity was enriched on raw wheat straw as the sole carbon source, which was able to transform lignocellulose into carboxylates under anaerobic conditions. Relatively high diversity levels are still observed despite the use of enrichment steps when working from environmental samples, likely due to the high functional redundancy observed in environmental microbial communities, being

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1464-429: A high-throughput manner provides efficient methods for addressing the functional potential of individual microorganisms as well as of whole communities in their natural habitats. Multiomics technologies including meta transcriptome , meta proteome and metabolome approaches now provide detailed information on microbial activities in the environment. Based on the rich foundation of data, the cultivation of microbes, which

1586-505: A keratinolytic microbial consortium pre-enriched from a soil sample. An appropriate dilution regime (10 ) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to

1708-599: A key asset of their functional stability. This intrinsic diversity may stand as a bottleneck in attempts to move forward to practical application due to (i) potential negative correlation with efficiency, (ii) real microbial cheaters whose presence has no impacts on degradation, (iii) security threats posed by the presence of known or unknown pathogens, and (iv) risks of losing the properties of interest if supported by rare taxa. Utilization of microbial consortia with less complexity, but equal efficiency, can lead to more controlled and optimized industrial processes. For instance,

1830-472: A lack of contemporaneous evidence. Several theories exist about what Hellenic dialect groups may have existed between the divergence of early Greek-like speech from the common Proto-Indo-European language and the Classical period. They have the same general outline but differ in some of the detail. The only attested dialect from this period is Mycenaean Greek , but its relationship to the historical dialects and

1952-843: A large proportion of functional genes were remarkably altered and the efficiency of diesel biodegradation was increased by reducing the biodiversity of a microbial community from diesel-contaminated soils. Therefore, it is crucial to find reliable strategies to narrow down the diversity toward optimized microbial consortia gained from environmental samples. A reductive-screening approach was applied to construct effective minimal microbial consortia for lignocellulose degradation based on different metabolic functional groups. Additionally, artificial selection approaches (dilution, toxicity, and heat) have been also employed to obtain bacterial consortia. Among them, dilution-to-extinction has already proven its efficiency for obtaining functional microbial consortia from seawater and rumen liquor . Dilution-to-extinction

2074-419: A lesser degree. Pamphylian Greek , spoken in a small area on the southwestern coast of Anatolia and little preserved in inscriptions, may be either a fifth major dialect group, or it is Mycenaean Greek overlaid by Doric, with a non-Greek native influence. Regarding the speech of the ancient Macedonians diverse theories have been put forward, but the epigraphic activity and the archaeological discoveries in

2196-474: 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. However, many other microbiome definitions have been published in recent decades. By 2020 the most cited definition was by Lederberg , and described microbiomes within an ecological context as a community of commensal , symbiotic , and pathogenic microorganisms within

2318-547: A number of nonmammalian taxa. Other analyses have found substantial variation in phylosymbiotic signals among mammalian taxa, sometimes with conflicting results. The presence of a robust phylosymbiotic correlation implies that host factors control microbial assembly . Even if the specific mechanisms are unknown, variation in the strength or presence of a measurable phylosymbiotic signal across host phylogeny could prove useful for identifying such mechanisms through comparative studies. However, as of 2020 most studies have focused on just

2440-543: A prefix /e-/, called the augment . This was probably originally a separate word, meaning something like "then", added because tenses in PIE had primarily aspectual meaning. The augment is added to the indicative of the aorist, imperfect, and pluperfect, but not to any of the other forms of the aorist (no other forms of the imperfect and pluperfect exist). The two kinds of augment in Greek are syllabic and quantitative. The syllabic augment

2562-695: A semantically and scientifically better term. Microbes interact with one another, and these symbiotic interactions have diverse consequences for microbial fitness, population dynamics, and functional capacities within the microbiome. The microbial interactions can either be between microorganisms of the same species or between different species, genera, families, and domains of life. The interactions can be separated into positive, negative, and neutral types. Positive interactions include mutualism , synergism , and commensalism . Negative interactions include amensalism , predation , parasitism , antagonism , and competition. Neutral interactions are interactions where there

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2684-671: A separate historical stage, though its earliest form closely resembles Attic Greek , and its latest form approaches Medieval Greek , and Koine may be classified as Ancient Greek in a wider sense. There were several regional dialects of Ancient Greek; Attic Greek developed into Koine. Ancient Greek was a pluricentric language , divided into many dialects. The main dialect groups are Attic and Ionic , Aeolic , Arcadocypriot , and Doric , many of them with several subdivisions. Some dialects are found in standardized literary forms in literature , while others are attested only in inscriptions. There are also several historical forms. Homeric Greek

2806-527: 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

2928-409: A shift towards a holistic approach in the coevolutions theory. The holistic approach sees the host and its associated microbiota as one unit (the so-called holobiont ), that coevolves as one entity. According to the holistic approach, holobiont's disease state is linked to dysbiosis , low diversity of the associated microbiota, and their variability: a so-called pathobiome state. The healthy state, on

3050-609: A standard subject of study in educational institutions of the Western world since the Renaissance . This article primarily contains information about the Epic and Classical periods of the language, which are the best-attested periods and considered most typical of Ancient Greek. From the Hellenistic period ( c.  300 BC ), Ancient Greek was followed by Koine Greek , which is regarded as

3172-510: A vowel or /n s r/ ; final stops were lost, as in γάλα "milk", compared with γάλακτος "of milk" (genitive). Ancient Greek of the classical period also differed in both the inventory and distribution of original PIE phonemes due to numerous sound changes, notably the following: The pronunciation of Ancient Greek was very different from that of Modern Greek . Ancient Greek had long and short vowels ; many diphthongs ; double and single consonants; voiced, voiceless, and aspirated stops ; and

3294-556: Is a literary form of Archaic Greek (derived primarily from Ionic and Aeolic) used in the epic poems , the Iliad and the Odyssey , and in later poems by other authors. Homeric Greek had significant differences in grammar and pronunciation from Classical Attic and other Classical-era dialects. The origins, early form and development of the Hellenic language family are not well understood because of

3416-418: Is added to stems beginning with consonants, and simply prefixes e (stems beginning with r , however, add er ). The quantitative augment is added to stems beginning with vowels, and involves lengthening the vowel: Some verbs augment irregularly; the most common variation is e → ei . The irregularity can be explained diachronically by the loss of s between vowels, or that of the letter w , which affected

3538-489: Is another relatively well-studied marine host to microbes. These three centimetre long worms reside within shallow marine sediments of the Mediterranean Sea. The worms do not contain a mouth or a digestive or excretory system, but are instead nourished with the help of a suite of extracellular bacterial endosymbionts that reside upon coordinated use of sulfur present in the environment. This system has benefited from some of

3660-644: Is called 'East Greek'. Arcadocypriot apparently descended more closely from the Mycenaean Greek of the Bronze Age. Boeotian Greek had come under a strong Northwest Greek influence, and can in some respects be considered a transitional dialect, as exemplified in the poems of the Boeotian poet Pindar who wrote in Doric with a small Aeolic admixture. Thessalian likewise had come under Northwest Greek influence, though to

3782-448: Is considered by some linguists to have been closely related to Greek . Among Indo-European branches with living descendants, Greek is often argued to have the closest genetic ties with Armenian (see also Graeco-Armenian ) and Indo-Iranian languages (see Graeco-Aryan ). Ancient Greek differs from Proto-Indo-European (PIE) and other Indo-European languages in certain ways. In phonotactics , ancient Greek words could end only in

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3904-480: Is expected to provide more advantages compared to conventional isolation and assembly as it (i) generates many microbial combinations ready to be screened, (ii) includes strains from the initial microbial pool that might be lost due to cultivation/isolation biases, and (iii) ensures that all microbes are physically present and interacting spontaneously. Microbialites are lithified microbial mats that grow in benthic freshwater and marine environments. Microbialites are

4026-521: Is increasingly evident that when a microbial consortium — two or more interacting microorganisms — is involved, additive or synergistic results can be expected. This occurs, in part, due to the fact that multiple species can perform a variety of tasks in an ecosystem like the plant root rhizosphere . Beneficial mechanisms of plant growth stimulation include enhanced nutrient availability, phytohormone modulation, biocontrol , biotic and abiotic stress tolerance) exerted by different microbial players within

4148-548: Is more controversial. Whipps's "theatre of activity" includes the essential role secondary metabolites play in mediating complex interspecies interactions and ensuring survival in competitive environments. Quorum sensing induced by small molecules allows bacteria to control cooperative activities and adapts their phenotypes to the biotic environment, resulting, e.g., in cell-cell adhesion or biofilm formation. All animals and plants form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In

4270-634: 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. The microbiomes of diverse marine animals are currently under study, from simplistic organisms including sponges and ctenophores to more complex organisms such as sea squirts and sharks. The relationship between

4392-432: Is needed to help identify the large fraction of unknown sequences obtained from metagenomics analyses, which for poorly studied ecosystems can be more than 70%. Depending on the applied method, even in well-studied microbiomes, 40–70% of the annotated genes in fully sequenced microbial genomes have no known or predicted function. As of 2019, 85 of the then established 118 phyla had not had a single species described, presenting

4514-569: Is no observed effect on the functional capacities or fitness of interacting species microbial life strategy concepts. Microbiomes exhibit different adaptive strategies . 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

4636-520: Is sometimes used to refer to the collective genomes of resident microorganisms; the term human metagenome has the same meaning. Humans are colonised by many microorganisms, with approximately the same order of magnitude of non-human cells as human cells. Some microorganisms that colonize humans are commensal , meaning they co-exist without harming or benefiting humans; others have a mutualistic relationship with their human hosts. Conversely, some non- pathogenic microorganisms can harm human hosts via

4758-480: Is still far from trivial due to large diversity and the effect of biotic interactions . Keratins are recalcitrant fibrous materials with cross-linked components, representing the most abundant proteins in epithelial cells . They are estimated to have considerable economic value after biodegradation . An efficient keratinolytic microbial consortium (KMCG6) was previously enriched from an environmental sample through cultivation in keratin medium. Despite reducing

4880-745: The Greek region of Macedonia during the last decades has brought to light documents, among which the first texts written in Macedonian , such as the Pella curse tablet , as Hatzopoulos and other scholars note. Based on the conclusions drawn by several studies and findings such as Pella curse tablet , Emilio Crespo and other scholars suggest that ancient Macedonian was a Northwest Doric dialect , which shares isoglosses with its neighboring Thessalian dialects spoken in northeastern Thessaly . Some have also suggested an Aeolic Greek classification. The Lesbian dialect

5002-497: The Hawaiian bobtail squid and the bioluminescent bacterium Aliivibrio fischeri is one of the best studied symbiotic relationships in the sea and is a choice system for general symbiosis research. This relationship has provided insight into fundamental processes in animal-microbial symbioses, and especially biochemical interactions and signaling between the host and bacterium. The gutless marine oligochaete worm Olavius algarvensis

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5124-409: The copiotrophs , which thrive in much higher carbon concentrations, and do well in high organic substrate conditions such as sewage lagoons. In addition to oligotrophic and copiotrophic strategists, the competitor–stress tolerator–ruderals framework can influence the outcomes of interactions. For example, microorganisms competing for the same source can also benefit from each other when competing for

5246-451: The first pronouncing the dynamic character of the microbiome, and the second clearly separating the term microbiota from the term microbiome . The microbiota consists of 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. The integration of phages , viruses , plasmids , and mobile genetic elements

5368-484: The metabolites they produce, like trimethylamine , which the human body converts to trimethylamine N-oxide via FMO3 -mediated oxidation. Certain microorganisms perform tasks that are known to be useful to the human host, but the role of most of them is not well understood. Those that are expected to be present, and that under normal circumstances do not cause disease, are sometimes deemed normal flora or normal microbiota . The Human Microbiome Project (HMP) took on

5490-501: The present , future , and imperfect are imperfective in aspect; the aorist , present perfect , pluperfect and future perfect are perfective in aspect. Most tenses display all four moods and three voices, although there is no future subjunctive or imperative. Also, there is no imperfect subjunctive, optative or imperative. The infinitives and participles correspond to the finite combinations of tense, aspect, and voice. The indicative of past tenses adds (conceptually, at least)

5612-441: 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). As of 2020, the emergence in publications about opportunistic pathogens and pathobionts has produced

5734-1031: The 5th century BC. Ancient pronunciation cannot be reconstructed with certainty, but Greek from the period is well documented, and there is little disagreement among linguists as to the general nature of the sounds that the letters represent. /oː/ raised to [uː] , probably by the 4th century BC. Greek, like all of the older Indo-European languages , is highly inflected. It is highly archaic in its preservation of Proto-Indo-European forms. In ancient Greek, nouns (including proper nouns) have five cases ( nominative , genitive , dative , accusative , and vocative ), three genders ( masculine , feminine , and neuter ), and three numbers (singular, dual , and plural ). Verbs have four moods ( indicative , imperative , subjunctive , and optative ) and three voices (active, middle, and passive ), as well as three persons (first, second, and third) and various other forms. Verbs are conjugated through seven combinations of tenses and aspect (generally simply called "tenses"):

5856-490: The Archaic period of ancient Greek (see Homeric Greek for more details): Μῆνιν ἄειδε, θεά, Πηληϊάδεω Ἀχιλῆος οὐλομένην, ἣ μυρί' Ἀχαιοῖς ἄλγε' ἔθηκε, πολλὰς δ' ἰφθίμους ψυχὰς Ἄϊδι προΐαψεν ἡρώων, αὐτοὺς δὲ ἑλώρια τεῦχε κύνεσσιν οἰωνοῖσί τε πᾶσι· Διὸς δ' ἐτελείετο βουλή· ἐξ οὗ δὴ τὰ πρῶτα διαστήτην ἐρίσαντε Ἀτρεΐδης τε ἄναξ ἀνδρῶν καὶ δῖος Ἀχιλλεύς. The beginning of Apology by Plato exemplifies Attic Greek from

5978-546: The Classical period of ancient Greek. (The second line is the IPA , the third is transliterated into the Latin alphabet using a modern version of the Erasmian scheme .) Ὅτι [hóti Hóti μὲν men mèn ὑμεῖς, hyːmêːs hūmeîs,   Microbial consortium The concept of a consortium was first introduced by Johannes Reinke in 1872, and in 1877 the term symbiosis

6100-417: The ability to study host–microbiome interactions with a low diversity microbial consortium, and it also offers a number of host and microbial genomic resources Corals are one of the more common examples of an animal host whose symbiosis with microalgae can turn to dysbiosis, and is visibly detected as bleaching. Coral microbiomes have been examined in a variety of studies, which demonstrate how variations in

6222-550: The aorist. Following Homer 's practice, the augment is sometimes not made in poetry , especially epic poetry. The augment sometimes substitutes for reduplication; see below. Almost all forms of the perfect, pluperfect, and future perfect reduplicate the initial syllable of the verb stem. (A few irregular forms of perfect do not reduplicate, whereas a handful of irregular aorists reduplicate.) The three types of reduplication are: Irregular duplication can be understood diachronically. For example, lambanō (root lab ) has

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6344-416: The assemblage of living microorganisms present in a defined environment. As phages, viruses, plasmids, prions, viroids, and free DNA are usually not considered as living microorganisms, they do not belong to the microbiota. The term microbiome, as it was originally postulated by Whipps and coworkers, includes not only the community of the microorganisms but also their "theatre of activity". The latter involves

6466-419: The augment when it was word-initial. In verbs with a preposition as a prefix, the augment is placed not at the start of the word, but between the preposition and the original verb. For example, προσ(-)βάλλω (I attack) goes to προσ έ βαλoν in the aorist. However compound verbs consisting of a prefix that is not a preposition retain the augment at the start of the word: αὐτο(-)μολῶ goes to ηὐ τομόλησα in

6588-484: The brain (previously believed to be sterile), with metagenomic evidence suggesting the species found may be enteric in origin. As the species found appear to be well-established, have no discernible impact on human health, and are species known to form consortia when found in the gut, it is highly likely they have also formed a symbiotic consortium within the brain. Synthetic microbial consortia (commonly called co-cultures) are multi-population systems that can contain

6710-438: The center of Greek scholarship, this division of people and language is quite similar to the results of modern archaeological-linguistic investigation. One standard formulation for the dialects is: West vs. non-West Greek is the strongest-marked and earliest division, with non-West in subsets of Ionic-Attic (or Attic-Ionic) and Aeolic vs. Arcadocypriot, or Aeolic and Arcado-Cypriot vs. Ionic-Attic. Often non-West

6832-443: The composition of these members, thus providing one of the first glimpses at a multi-domain marine animal symbiosis. The gammaproteobacterium Endozoicomonas is emerging as a central member of the coral's microbiome, with flexibility in its lifestyle. Given the recent mass bleaching occurring on reefs, corals will likely continue to be a useful and popular system for symbiosis and dysbiosis research. Sponges are common members of

6954-589: The concept of Candidatus species would be extended to the groups of closely related genome sequences, and their names would be published following established rules of bacterial nomenclature . 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. Ancient Greek language Ancient Greek ( Ἑλληνῐκή , Hellēnikḗ ; [hellɛːnikɛ́ː] ) includes

7076-500: 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. Discovery of DNA , the development of sequencing technologies , PCR , and cloning techniques enabled the investigation of microbial communities using cultivation-independent, DNA and RNA -based approaches. A further important step

7198-419: The critical roles of microbes in human, animal, and plant health. These have revolutionised microbial ecology . The analysis of genomes and metagenomes in a high-throughput manner now provide highly effective methods for researching the functioning of both individual microorganisms as well as whole microbial communities in natural habitats. Microbiome research originated in microbiology and started back in

7320-427: The definition of the microbiome. 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, amended with

7442-420: The development of sequencing technologies , PCR , and cloning techniques enabled the investigation of microbial communities using cultivation-independent approaches. Further paradigm shifts occurred at the beginning of this century and still continue, as new sequencing technologies and accumulated sequence data have highlighted both the ubiquity of microbial communities in association within higher organisms and

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7564-611: The dialect of Sparta ), and Northern Peloponnesus Doric (including Corinthian ). All the groups were represented by colonies beyond Greece proper as well, and these colonies generally developed local characteristics, often under the influence of settlers or neighbors speaking different Greek dialects. After the conquests of Alexander the Great in the late 4th century BC, a new international dialect known as Koine or Common Greek developed, largely based on Attic Greek , but with influence from other dialects. This dialect slowly replaced most of

7686-478: The diverse hierarchies of interactions of microbes with one another and with the host biotic and abiotic environments. Many current definitions fail to capture this complexity and describe the term microbiome as encompassing the genomes of microorganisms only. In 2020, a panel of international experts, organised by the EU-funded MicrobiomeSupport project, published the results of their deliberations on

7808-569: The earliest known fossilised evidence of life, dating back 3.7 billion years. Today modern microbialites are scarce, and are formed mainly by Pseudomonadota (formerly Proteobacteria), cyanobacteria , sulphate-reducing bacteria , diatoms , and microalgae . These microorganisms produce adhesive compounds that cement sand and join other rocky materials to form mineral " microbial mats ". The mats build layer by layer, growing gradually over time. Although various studies have shown that single microorganisms can exert beneficial effects on plants, it

7930-463: The ecology and physiology of plants. The core plant microbiome is thought to contain keystone microbial taxa essential for plant health and for the fitness of the plant holobiont . Likewise, the mammalian gut microbiome has emerged as a key regulator of host physiology, and coevolution between host and microbial lineages has played a key role in the adaptation of mammals to their diverse lifestyles. Microbiome research originated in microbiology back in

8052-415: The ecology of rhizosphere microorganisms provided the first definition of the term microbiome. 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

8174-423: The environment to enhance polymer degradation. Two approaches exist to obtain microbial consortia involving either (i) a synthetic assembly from scratch by combining several isolated strains, or (ii) obtainment of complex microbial communities from environmental samples. For the later, enrichment process is often used to get the desired microbial consortia. For instance, a termite gut-derived consortium showing

8296-470: The exception rather than the rule in vertebrates. Meta-analyses of fish  and birds  have failed to detect the strength of correlations to diet and phylogeny reported in mammals. A recent analysis of samples from more than 100 vertebrate species also found the strength of phylogenetic correlation to be much higher in mammals than in birds, reptiles, amphibians, or fish. It is increasingly appreciated in nonvertebrate animals that fundamental aspects of

8418-459: The exhaled breath or "blow" of cetaceans can provide an assessment of their state of health. Blow is composed of a mixture of microorganisms and organic material , including lipids , proteins , and cellular debris derived from the linings of the airways which, when released into the relatively cooler outdoor air, condense to form a visible mass of vapor, which can be collected. There are various methods for collecting exhaled breath samples, one of

8540-424: The extent to which these concepts, developed for macro- eukaryotes , can be applied to prokaryotes with their different lifestyles regarding dormancy , variation of phenotype , and horizontal gene transfer as well as to micro-eukaryotes that is not quite clear. This raises the challenge of considering an entirely novel body of conceptual ecology models and theory for microbiome ecology, particularly in relation to

8662-453: The first microscopes allowed the discovery of a new, unknown world and led to the identification of microorganisms . Access to the previously invisible world opened the eyes and the minds of the researchers of the seventeenth century. Antonie van Leeuwenhoek investigated diverse bacteria of various shapes, fungi , and protozoa , which he called animalcules , mainly from water, mud, and dental plaque samples, and discovered biofilms as

8784-452: The fitness of the plant holobiont". 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. The health status of a plant has been reported in some studies to be reflected by or linked to its microbiome. Plant and plant-associated microbiota colonise different niches on and inside

8906-663: The forms of the Greek language used in ancient Greece and the ancient world from around 1500 BC to 300 BC. It is often roughly divided into the following periods: Mycenaean Greek ( c.  1400–1200 BC ), Dark Ages ( c.  1200–800 BC ), the Archaic or Epic period ( c.  800–500 BC ), and the Classical period ( c.  500–300 BC ). Ancient Greek was the language of Homer and of fifth-century Athenian historians, playwrights, and philosophers . It has contributed many words to English vocabulary and has been

9028-436: The growing climate-related and anthropogenic-induced changes already impacting the ocean. The plant microbiome plays key roles in plant health and food production and has received significant attention in recent years. Plants live in association with diverse microbial consortia , referred to as the plant microbiota , living both inside (the endosphere ) and outside (the episphere) of plant tissues. They play important roles in

9150-450: The gut microbiomes across mammals. The vertebrate adaptive immune system is even speculated to have evolved as just such a factor for selective maintenance of symbiotic homeostasis . The importance of phylogeny-correlated factors to the diversity of vertebrate microbiomes more generally is still poorly understood. Phylosymbiosis , or the observation that more closely related host species have more similar microbiomes, has been described in

9272-556: The historical Dorians . The invasion is known to have displaced population to the later Attic-Ionic regions, who regarded themselves as descendants of the population displaced by or contending with the Dorians. The Greeks of this period believed there were three major divisions of all Greek people – Dorians, Aeolians, and Ionians (including Athenians), each with their own defining and distinctive dialects. Allowing for their oversight of Arcadian, an obscure mountain dialect, and Cypriot, far from

9394-472: The historical circumstances of the times imply that the overall groups already existed in some form. Scholars assume that major Ancient Greek period dialect groups developed not later than 1120 BC, at the time of the Dorian invasions —and that their first appearances as precise alphabetic writing began in the 8th century BC. The invasion would not be "Dorian" unless the invaders had some cultural relationship to

9516-403: The host's relationship to its symbiotic community can change drastically between taxa: many insects depend entirely on microbes for key metabolites , while others seem to be devoid of resident gut microbes. The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including

9638-437: The initial consortium, showing that simplification can be achieved without loss of function and efficiency. As shown in the diagram on the right, the workflow for this study included four steps: (1) Enrichment for the desired traits e.g., keratinolytic activity by selection in keratin medium, where keratin is the sole carbon source. This process was evaluated by functional assessments (cell density, enzymes activity, and ratio of

9760-410: The microbial diversity during the enrichment process, KMCG6 still included several OTUs scattered amongst seven bacterial genera. In 2020 Kang et al., using a strategy based on enrichment and dilution-to-extinction cultures, extracted from this original consortium (KMCG6) a simplified microbial consortia (SMC) with fewer species but similar keratinolytic activity. Serial dilutions were performed on

9882-408: The microbiome is always composed by all members, which interact with each other, live in the same habitat, and form their ecological niche together. The well-established term virome is derived from virus and genome and is used to describe viral shotgun metagenomes consisting of a collection of nucleic acids associated with a particular ecosystem or holobiont . Viral metagenomes can be suggested as

10004-440: The microbiome of the skin of marine mammals looks like under typical conditions allows understanding of how these communities different from free microbial communities found in the sea. Cetaceans are in danger because they are affected by multiple stress factors which make them more vulnerable to various diseases. They have been high susceptibility to airway infections, but little is known about their respiratory microbiome. Sampling

10126-543: The microbiome. 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 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

10248-418: The microbiome. The integration of phages , viruses , plasmids , and mobile genetic elements is a more controversial issue in the definition of the microbiome. There is also no clear consensus as to whether extracellular DNA derived from dead cells, so-called "relic DNA", belongs to the microbiome. Relic DNA can be up to 40% of the sequenced DNA in soil, and was up to 33% of the total bacterial DNA on average in

10370-423: The microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al. , but supplemented with two explanatory paragraphs,

10492-637: The most recent is through the use of aerial drones. This method provides a safer, quieter, and less invasive alternative and often a cost-effective option for monitoring fauna and flora. Blow samples are taken to the laboratory where the respiratory tract microbiota are amplified and sequenced. The use of aerial drones has been more successful with large cetaceans due to slow swim speeds and larger blow sizes. The plant microbiome plays roles in plant health and food production and has received significant attention in recent years. Plants live in association with diverse microbial consortia . These microbes, referred to as

10614-409: The most sophisticated 'omics and visualization tools. For example, multi-labeled probing has improved visualization of the microbiome and transcriptomics and proteomics have been applied to examine host–microbiome interactions, including energy transfer between the host and microbes and recognition of the consortia by the worm's innate immune system. The major strength of this system is that it does offer

10736-403: The nineteenth century, microbial ecology started with the pioneering work by Martinus W. Beijerinck and Sergei Winogradsky . The newly established science of environmental microbiology resulted in another paradigm shift: microorganisms are everywhere in natural environments, often associated with hosts and, for the first time, beneficial effects on their hosts were reported. Subsequently,

10858-410: The ocean environment, most notably temperature, light, and inorganic nutrients, affect the abundance and performance of the microalgal symbionts, as well as calcification and physiology of the host. Studies have also suggested that resident bacteria, archaea, and fungi additionally contribute to nutrient and organic matter cycling within the coral, with viruses also possibly playing a role in structuring

10980-565: 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. 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. Sponge microbiomes are composed of specialists and generalists, and complexity of their microbiome appears to be shaped by host phylogeny. Studies have shown that

11102-534: 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

11224-499: The older dialects, although the Doric dialect has survived in the Tsakonian language , which is spoken in the region of modern Sparta. Doric has also passed down its aorist terminations into most verbs of Demotic Greek . By about the 6th century AD, the Koine had slowly metamorphosed into Medieval Greek . Phrygian is an extinct Indo-European language of West and Central Anatolia , which

11346-464: The organisms behind. For example, 154,723 microbial genomes of the global human microbiome were reconstructed in 2019 from 9,428 metagenomes. Computational modeling of microbiomes has been used to complement experimental methods for investigating microbial function by utilizing multi-omic data to predict complex inter-species and host-species dynamics. A popular in silico method is to combine metabolic network models of microbial taxa present in

11468-625: The other hand, beneficial microbial interactions promote plant growth. The mammalian gut microbiome has emerged as a key regulator of host physiology , and coevolution between host and microbial lineages has played a key role in the adaptation of mammals to their diverse lifestyles. Diet, especially herbivory , is an important correlate of microbial diversity in mammals. Most mammalian microbiomes are also strongly correlated with host phylogeny , despite profound shifts in diet. This suggests host factors that themselves change across host phylogeny, such as gut physiology, play an important role in structuring

11590-442: The other hand, is accompanied with eubiosis , high diversity, and uniformity of the respective microbiota. 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

11712-442: The other hand. Metagenome data provides a playground for new predictions, yet much more data is needed to strengthen the links between sequence and rigorous functional predictions. This becomes obvious when considering that the replacement of one single amino acid residue by another may lead to a radical functional change, resulting in an incorrect functional assignment to a given gene sequence. Additionally, cultivation of new strains

11834-409: The past century has shown only a small proportion of microorganisms are associated with disease or pathogenicity. The overwhelming majority of microbes are essential for ecosystem functioning and known for beneficial interactions with other microbes as well as macroorganisms. In fact, maintaining a healthy microbiome is essential for human health and may be a target for new therapeutics. At the end of

11956-487: The perfect stem eilēpha (not * lelēpha ) because it was originally slambanō , with perfect seslēpha , becoming eilēpha through compensatory lengthening. Reduplication is also visible in the present tense stems of certain verbs. These stems add a syllable consisting of the root's initial consonant followed by i . A nasal stop appears after the reduplication in some verbs. The earliest extant examples of ancient Greek writing ( c.  1450 BC ) are in

12078-426: The plant defense system against pathogens, promoting nutrient uptake, and enhancing tolerance to different environmental stresses. Rhizosphere microorganisms can influence one another, and the resulting consortia of PGPB + PGPB (e.g., a nitrogen-fixing bacterium such as Rhizobium spp. and Pseudomonas fluorescens ), AMF + PGPB, and Trichoderma + PGPB may have synergetic effects on plant growth and fitness, providing

12200-420: 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

12322-567: The plant with enhanced benefits to overcome biotic and abiotic stress. Dashed arrows indicate beneficial interactions between AMF and Trichoderma. The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owing to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities

12444-423: The plant's microbiota , live both inside (the endosphere ) and outside (the episphere ) of plant tissues , and play important roles in the ecology and physiology of plants. "The core plant microbiome is thought to comprise keystone microbial taxa that are important for plant fitness and established through evolutionary mechanisms of selection and enrichment of microbial taxa containing essential functions genes for

12566-426: 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. It reached a milestone in 2012 when it published its initial results. Currently available methods for studying microbiomes, so-called multi-omics , range from high throughput isolation ( culturomics ) and visualization ( microscopy ), to targeting

12688-450: The residual substrate) and compositional analysis. (2) Serial dilutions were conducted to the enriched effective microbial consortia. Six dilutions were prepared, from dilution 10 to 10 with 24 replicates. The dissimilarity between dilutions was evaluated by Euclidean distance calculation based on functional assessment criteria. (3) Library construction was done from the dilution offering the optimal dissimilarity among replicates. Dilution 10

12810-417: The rhizosphere, such as plant-growth-promoting bacteria (PGPB) and fungi such as Trichoderma and Mycorrhizae . The diagram on the right illustrates that rhizosphere microorganisms like plant-growth-promoting bacteria (PGPB), arbuscular mycorrhizal fungi (AMF), and fungi from the genus Trichoderma spp. can establish beneficial interactions with plants, promoting plant growth and development, increasing

12932-428: The same compound at different trophic levels . Stability of a complex microbial ecosystem depends on trophic interactions for the same substrate at different concentration levels. As of 2020 microbial social adaptations in nature have been understudied. Here molecular markers can provide insight into social adaptations by supporting the theories, e.g., of altruists and cheaters in native microbiomes. According to

13054-399: The scientific literature, but these terms do not refer to biomes (a regional ecosystem with a distinct assemblage of (micro) organisms, and physical environment often reflecting a certain climate and soil) as the microbiome itself. Consequently, it would be better to use the original terms (bacterial, archaeal, or fungal community). In contrast to the microbiota, which can be studied separately,

13176-870: The seventeenth century. The development of new techniques and equipment boosted microbiological research and caused paradigm shifts in understanding health and disease. The development of the first microscopes allowed the discovery of a new, unknown world and led to the identification of microorganisms. Infectious diseases became the earliest focus of interest and research. However, only a small proportion of microorganisms are associated with disease or pathogenicity. The overwhelming majority of microbes are essential for healthy ecosystem functioning and known for beneficial interactions with other microbes and organisms. 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. Discovery of DNA ,

13298-434: 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

13420-415: The skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa , conjunctiva , biliary tract , and gastrointestinal tract . Types of human microbiota include bacteria , archaea , fungi , protists and viruses . Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics , the term human microbiome

13542-775: The sponge microbiome contributes to nitrogen cycling in the oceans, especially through the oxidation of ammonia by archaea and bacteria. Most recently, microbial symbionts of tropical sponges were shown to produce and store polyphosphate granules, perhaps enabling the host to survive periods of phosphate depletion in oligotrophic marine environments. The microbiomes of some sponge species do appear to change in community structure in response to changing environmental conditions, including temperature and ocean acidification, as well as synergistic impacts. Cetacean microbiomes can be difficult to assess because of difficulties accessing microbial samples. For example, many whale species are rare and are deep divers. There are different techniques for sampling

13664-517: The syllabic script Linear B . Beginning in the 8th century BC, however, the Greek alphabet became standard, albeit with some variation among dialects. Early texts are written in boustrophedon style, but left-to-right became standard during the classic period. Modern editions of ancient Greek texts are usually written with accents and breathing marks , interword spacing , modern punctuation , and sometimes mixed case , but these were all introduced later. The beginning of Homer 's Iliad exemplifies

13786-467: The taxonomic composition ( metabarcoding ), or addressing the metabolic potential ( metabarcoding of functional genes, metagenomics ) to analyze microbial activity ( metatranscriptomics , metaproteomics , metabolomics ). Based on metagenome data, microbial genomes can be reconstructed. While first metagenome-assembled genomes were reconstructed from environmental samples, in recent years, several thousands of bacterial genomes were binned without culturing

13908-488: The term microbiome, but are not a part of microbiota. The term microbiome is also sometimes confused with the metagenome . Metagenome is, however, clearly defined as a collection of genomes and genes from the members of a microbiota. 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 bacteriome , archaeome , mycobiome , or virome have started appearing in

14030-454: The whole spectrum of molecules produced by the microorganisms, including their structural elements (nucleic acids, proteins, lipids, polysaccharides), metabolites (signalling molecules, toxins, organic, and inorganic molecules), and molecules produced by coexisting hosts and structured by the surrounding environmental conditions. Therefore, all mobile genetic elements, such as phages, viruses, and "relic" and extracellular DNA, should be included in

14152-475: Was Aeolic. For example, fragments of the works of the poet Sappho from the island of Lesbos are in Aeolian. Most of the dialect sub-groups listed above had further subdivisions, generally equivalent to a city-state and its surrounding territory, or to an island. Doric notably had several intermediate divisions as well, into Island Doric (including Cretan Doric ), Southern Peloponnesus Doric (including Laconian ,

14274-499: Was first used by J.L. Mohr in 1952 in The Scientific Monthly to mean the microorganisms found in a specific environment. 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. In 1988, Whipps and colleagues working on

14396-428: 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 microbial communities in association within higher organisms and the critical roles of microbes in human, animal, and plant health. These new possibilities have revolutionized microbial ecology , because the analysis of genomes and metagenomes in

14518-778: Was introduced and later expanded on. Evidence for symbiosis between microbes strongly suggests it to have been a necessary precursor of the evolution of land plants and for their transition from algal communities in the sea to land. Microbes hold promising application potential to raise the efficiency of bioprocesses when dealing with substances that are resistant to decomposition. A large number of microorganisms have been isolated based on their ability to degrade recalcitrant materials such as lignocellulose and polyurethanes. In many cases of degradation efficiency, microbial consortia have been found superior when compared to single strains. For example, novel thermophilic consortia of Brevibacillus spp. and Aneurinibacillus sp. have been isolated from

14640-422: Was often ignored or underestimated over the last thirty years, has gained new importance, and high throughput culturomics is now an important part of the toolbox to study microbiomes. The high potential and power of combining multiple "omics" techniques to analyze host-microbe interactions are highlighted in several reviews. The word microbiome (from the Greek micro meaning "small" and bíos meaning "life")

14762-449: Was selected to construct the SMC library in this case. (4) Selection of the most promising SMC is based on functional and compositional characterization. Consortia are commonly found in humans, with the predominant examples being the skin consortium and the intestinal consortium which provide protection and aid in human nutrition. Additionally, bacteria have been identified as existing within

14884-471: Was the introduction of phylogenetic markers such as the 16S rRNA gene for microbial community analysis by Carl Woese and George E. Fox in 1977. Nowadays biologists can barcode bacteria, archaea , fungi , algae , and protists in their natural habitats, e.g., by targeting their 16S and 18S rRNA genes, internal transcribed spacer (ITS), or, alternatively, specific functional regions of genes coding for specific enzymes. Another major paradigm shift

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