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Phage/virus receptor locations in Gram-positive Bacteria, Gram-negative Bacteria, and two types of Archaea. Cell wall and membrane structures are depicted for select classic groups of Bacteria and Archaea (i.e. mesophilic Archaea noted for colonizing humans). Known phage/virus receptor sites are indicated by stars. Note that most of the components to which bacterial phages attach (peptidoglycans, lipopolysaccharides, lipoteichoic acid, and fatty acid D-glycerol ester phospholipids) are absent in Archaea. Although both Bacteria and Archaea possess membrane proteins and pili, they are not highly conserved between these Domains of life.
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Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of disease-causing Archaea is due, in part, to mutually-exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association o...
Contexts in source publication
Context 1
... recognize their hosts via extra- cellular receptors that can be located in the outer membrane of Gram-negative Bacteria, in the cell wall of Gram- positive Bacteria or associated with the flagella or the pili of both Gram- positive and Gram-negative species [46] (Fig. 1). The mycobacterial phages that have been characterized bind to glycolipids that are attached to the out- side of peptidoglycan and arabinogalac- tan cell wall [47]. The portion of each phage that recognizes and binds to a receptor is also highly variable, even among phages that have similar recep- tors on their hosts [46]. Receptors ...Context 2
... have been described). Archaeal flagella also appear to have a different ancestry, and possess many divergent characteristics (such as N-linked glycans vs. O-linked glycans, and a different mode of assem- bly), from bacterial flagella [51]. Therefore, the structures that bacterial phages recognize and bind to are largely absent from archaeal cells (Fig. 1). Given that these components are required for phage infection, it seems unlikely that bacterial phages would be able to infect archaeal ...Citations
... However, this observation has been reported in Bacteria rather than Archaea. Although Archaea prophages have also been studied, Archaea pathogens have not yet been reported (39). ...
Phages and prophages are one of the principal modulators of microbial populations. However, much of their diversity is still poorly understood. Here, we extracted 33,624 prophages from 13,713 complete prokaryotic genomes to explore the prophage diversity and their relationships with their host. Our results reveal that prophages were present in 75% of the genomes studied. In addition, Enterobacterales were significantly enriched in prophages. We also found that pathogens are a significant reservoir of prophages. Finally, we determined that the prophage relatedness and the range of genomic hosts were delimited by the evolutionary relationships of their hosts. On a broader level, we got insights into the prophage population, identified in thousands of publicly available prokaryotic genomes, by comparing the prophage distribution and relatedness between them and their hosts.
IMPORTANCE Phages and prophages play an essential role in controlling their host populations either by modulating the host abundance or providing them with genes that benefit the host. The constant growth in next-generation sequencing technology has caused the development of powerful computational tools to identify phages and prophages with high precision. Making it possible to explore the prophage populations integrated into host genomes on a large scale. However, it is still a new and under-explored area, and efforts are still required to identify prophage populations to understand their dynamics with their hosts.
... General biotechnological interest particularly with respect to the identification of novel enzymes in various archaeal species has been growing up among the researchers due to their enormous adaptation capability to extreme environments [62,63]. Moreover, their ability to withstand high temperature makes them viable at high-temperature processes such as extrusion and microencapsulation [64] used especially for aquafeed. ...
The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.
... Another prospect is that the emergence of pathogenesis is a rare event that occurred in only a few bacteria and eukaryotes, but never in archaea 156 . Among the very few bacterial pathogens (estimated to comprise less than 1% of all bacterial species 158 ), pathogenic Gram-negative proteobacteria deliver virulence factors into their target cells by using specialized molecular needles such as type III secretion systems, which are absent from archaea. ...
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host–archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease. The archaeal community, the archaeome, is now increasingly recognized as an important component of host-associated microbiomes. In this Review, Moissl-Eichinger and colleagues discuss the diversity and potential roles of the archaea associated with protists, plants and animals, highlighting the potential roles of archaea in human health and disease.
... Archaea at the present Moreover, Gill and Brinkman (2011) published different hypothesis that Archaea may contribute to disease caused by other organisms indirectly. They presume Archaea may facilitate the growth of diseasecausing organisms rather than causing disease directly by themselves. ...
... Furthermore, there is hypothesized that virulence bacteriophages could not interact with Archaea, in this way hindering the ability of Archaea to become pathogens. The lack of gene exchange from bacteriophages to Archaea may explain why so few (if any) archaeal pathogens exist (Lawrence, 2005;Bennewies et al., 2006;Gill and Brinkman, 2011). ...
There are hundreds of organisms that infect and cause disease in humans and animals. These organisms can be bacteria and single-celled eukaryote, as well as a few parasites. Archaea, one of the three domain of life, immensely diverse group of prokaryotes and includes a number of “extremophiles” that develop in such environments as hot springs, salt lakes, human and animal gut, volcanic submarines and low, high pH habitats. It is puzzling that despite being one of the most numerous and ubiquitous life forms on earth, no member of the domain Archaea has been described as human or animal pathogen. The absence of pathogenic Archaea in the taxonomy database is statistically highly significant. The aim of this article is to display a brief overview of what is currently known about archaea and archaeal potential pathogenicity in and on human being and animals.
... However, the CCA results may also indicate, at least in part, a proportional lack of pathogens in some phyla, such as Crenarchaeota, Euryarchaeota, Verrucomicrobia, and Bacteroidetes [69]. Table 1 Li Environ Sci Eur (2019) 31:37 Archaea cannot easily absorb phage particles because of their extracellular structures, which differ from bacteria [70]. A recent study by Li et al. [9] also found that the five most abundant bacterial pathogens were from either Proteobacteria or Firmicutes in wastewater microbiomes. ...
Background
Human pathogens are widespread in the environment, and examination of pathogen-enriched environments in a rapid and high-throughput fashion is important for development of pathogen-risk precautionary measures. In this study, a Local BLASTP procedure for metagenomic screening of pathogens in the environment was developed using a toxin-centered database. A total of 69 microbiomes derived from ocean water, freshwater, soils, feces, and wastewater were screened using the Local BLASTP procedure. Bioinformatic analysis and Canonical Correspondence Analysis were conducted to examine whether the toxins included in the database were taxonomically associated.
Results
The specificity of the Local BLASTP method was tested with known and unknown toxin sequences. Bioinformatic analysis indicated that most toxins were phylum-specific but not genus-specific. Canonical Correspondence Analysis implied that almost all of the toxins were associated with the phyla of Proteobacteria, Nitrospirae and Firmicutes. Local BLASTP screening of the global microbiomes showed that pore-forming RTX toxin, ornithine carbamoyltransferase ArgK, and RNA interferase Rel were most prevalent globally in terms of relative abundance, while polluted water and feces samples were the most pathogen-enriched.
Conclusions
The Local BLASTP procedure was applied for rapid detection of toxins in environmental samples using a toxin-centered database built in this study. Screening of global microbiomes in this study provided a quantitative estimate of the most prevalent toxins and most pathogen-enriched environments. Feces-contaminated environments are of particular concern for pathogen risks.
... segmented/non-segmented, single/double stranded RNA/DNA, positive/negative sense) and particular groups show distinct affinity towards each respective domain [1]. Viruses exclusively associated with archaea and bacteria are commonly referred to as phages [1,3,15]. Phages have primarily single or double stranded DNA based genomes (designated Group II and Group I, respectively) that are on average smaller than those of viruses infecting eukaryotes [3]. ...
Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.
... [86][87][88][89] No pathogenic archaeal species has been identified so far, although their potential existence has been discussed for over a decade. [90][91][92][93] However, a role of archaea in inflammatory diseases such as periodontitis 94-96 , inflammatory bowel disease (IBD) 97 , or airway inflammation 98 has been suggested. The methanogenic archaeon Methanosphaera stadtmanae induces strong inflammatory responses in human peripheral blood mononuclear cells (PBMCs) 97 and moDCs 99 . ...
RNA‐sensing Toll‐like receptors (TLRs) are often described as antiviral receptors of the innate immune system. However, the past decade has shown that the function and relevance of these receptors are far more complex. They were found to be essential for the detection of various bacterial, archaeal, and eukaryotic microorganisms and facilitate the discrimination between dead and living microbes. The cytokine and interferon response profile that is triggered has the potential to improve the efficacy of next‐generation vaccines and may prevent the development of asthma and allergy. Nevertheless, the ability to recognize foreign RNA comes with a cost as also damaged host cells can release nucleic acids that might induce an inappropriate immune response. Thus, it is not surprising that RNA‐sensing TLRs play a key role in various autoimmune diseases. However, promising new inhibitors and antagonists are on the horizon to improve their treatment.
... vi) Moreover, as to date not a single archaeal pathogen is known, their medical relevance is considered negligible, resulting in a reduced effort to understand their role. As a consequence, the human archaeome remains uncharted territory of microbiome research, and many questions with respect to potential pathogenicity, function, and structural interactions with host and other microorganisms remain currently unanswered [5,[33][34][35][36][37][38]. ...
Forty years ago, archaea were described as a separate domain of life, distinct from bacteria and eukarya. Although it is known for quite a long time that methanogenic archaea are substantial components of the human gastrointestinal tract (GIT) and the oral cavity, the knowledge on the human archaeome is very limited. Various methodological problems contribute to the invisibility of the human archaeome, resulting in severe knowledge gaps and contradictory information. Similar to the bacteriome, the archaeal biogeography was found to be site-specific, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT landscape, (iii) a mixed skin/GIT landscape in nose, and (iv) a woesearchaeal lung landscape, including numerous unknown archaeal clades. Compared with so-called universal microbiome approaches, archaea-specific protocols reveal a wide diversity and high quantity of archaeal signatures in various human tissues, with up to 1 : 1 ratios of bacteria and archaea in appendix and nose samples. The archaeome interacts closely with the bacteriome and the human body cells, whereas the roles of the human-associated archaea with respect to human health are only sparsely described. Methanogenic archaea and methane production were correlated with many health issues, including constipation, periodontitis and multiple sclerosis. However, one of the most burning questions — do archaeal pathogens exist? — still remains obscure to date.
... In nutrient limited situations, bacteria could parasitize Archaea to access additional nutrients-and this could serve to sustain the community. Archaea are inevitably the victims as they are almost never implicated as parasites of other organisms ( Gill and Brinkman, 2011;Eckburg, Lepp and Relman, 2003). A rare case of ArchaeaArchaea parasitism is known where Nanoarchaeum equitans grows attached to the surface of the larger Ignicoccus spp., but Nanoarchaeum equitans does not become endoparasitic of its host ( Huber et al., 2002). ...
In this chapter we propose a model for the early evolution of eukaryotic cells under pressure of intense endoparasitism. Defining features of eukaryotes developed to defend against endoparasites (primarily bacteria), including a defensive system composed of an antioxidant sterol-enriched internal and external membrane system that could be used to entrap endoparasites and degrade them with superoxide produced on the membranes, cytoskeleton scaffolding for the membrane system, and a nuclear envelope to exclude endoparasites from reaching the genome. Mitochondria and chloroplasts evolved from the prokaryotes that developed ways to neutralize the reactive oxygen defense of the host. For mitochondria, hydrogen pumping to the exterior of the endoparasite enabled them to reduce superoxide to water, effectively defeating the host defense. Other features of eukaryotes that may have evolved from defense from endoparasitism include: autophagy, cell walls in fungi and plants, acquired immunity in animals, multicellularity, and apoptosis. We evaluate fossil data, where available, to provide additional information regarding the early evolution of eukaryotes and the prevalence of endoparasitic microbes.
... In nutrient-limited situations, bacteria could parasitize Archaea to access additional nutrients-and this could serve to sustain the community. Archaea are inevitably the victims as they are almost never implicated as parasites of other organisms (Gill and Brinkman, 2011;Eckburg et al., 2003). A rare case of ...
