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Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.
Gracilicutes is a clade in bacterial phylogeny.
Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) were first discovered in an extremely acidic mine located in northern California (Richmond Mine at Iron Mountain) by Brett Baker in Jill Banfield's laboratory at the University of California Berkeley. These novel groups of archaea named ARMAN-1, ARMAN-2 (Candidatus Micrarchaeum acidiphilum ARMAN-2), and ARMAN-3 were missed by previous PCR-based surveys of the mine community because the ARMANs have several mismatches with commonly used PCR primers for 16S rRNA genes. Baker et al. detected them in a later study using shotgun sequencing of the community. The three groups were originally thought to represent three unique lineages deeply branched within the Euryarchaeota, a subgroup of the Archaea. However, based on a more complete archaeal genomic tree, they were assigned to a new superphylum named DPANN. The ARMAN groups now comprise deeply divergent phyla named Micrarchaeota and Parvarchaeota. Their 16S rRNA genes differ by as much as 17% between the three groups. Prior to their discovery, all of the Archaea shown to be associated with Iron Mountain belonged to the order Thermoplasmatales (e.g., Ferroplasma acidarmanus).
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
An alarmone is an intracellular signal molecule that is produced in bacteria, chloroplasts, and a slim minority of archaea reacting to harsh environmental factors. They regulate the gene expression at transcription level. Alarmones are produced in high concentrations when harsh environmental factors occur in bacteria and plants, such as lack of amino acids, to produce proteins. Stringent factors take uncharged tRNA and convert it to an alarmone. Guanosine-5'-triphosphate (GTP) is then converted to 5´-diphosphate 3´-diphosphate guanosine (ppGpp), the archetypical alarmone. ppGpp will bind to RNA polymerase β and β´ subunits, changing promoter preference. It will decrease transcription of rRNA and other genes but will increase transcription of genes involved in amino acid biosyntheses and metabolisms involved in famine.
Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotic. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla as well as the phyla "Cyanobacteria", Chloroflexota, and Deinococcota.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
Nanohaloarchaea is a clade of diminutive archaea with small genomes and limited metabolic capabilities, belonging to the DPANN archaea. They are ubiquitous in hypersaline habitats, which they share with the extremely halophilic haloarchaea.
Biological dark matter is an informal term for unclassified or poorly understood genetic material. This genetic material may refer to genetic material produced by unclassified microorganisms. By extension, biological dark matter may also refer to the un-isolated microorganism whose existence can only be inferred from the genetic material that they produce. Some of the genetic material may not fall under the three existing domains of life: Bacteria, Archaea and Eukaryota; thus, it has been suggested that a possible fourth domain of life may yet be discovered, although other explanations are also probable. Alternatively, the genetic material may refer to non-coding DNA and non-coding RNA produced by known organisms.
Viral metagenomics uses metagenomic technologies to detect viral genomic material from diverse environmental and clinical samples. Viruses are the most abundant biological entity and are extremely diverse; however, only a small fraction of viruses have been sequenced and only an even smaller fraction have been isolated and cultured. Sequencing viruses can be challenging because viruses lack a universally conserved marker gene so gene-based approaches are limited. Metagenomics can be used to study and analyze unculturable viruses and has been an important tool in understanding viral diversity and abundance and in the discovery of novel viruses. For example, metagenomics methods have been used to describe viruses associated with cancerous tumors and in terrestrial ecosystems.
Poribacteria are a candidate phylum of bacteria originally discovered in the microbiome of marine sponges (Porifera). Poribacteria are Gram-negative primarily aerobic mixotrophs with the ability for oxidative phosphorylation, glycolysis, and autotrophic carbon fixation via the Wood – Ljungdahl pathway. Poribacterial heterotrophy is characterised by an enriched set of glycoside hydrolases, uronic acid degradation, as well as several specific sulfatases. This heterotrophic repertoire of poribacteria was suggested to be involved in the degradation of the extracellular sponge host matrix.
Parvarchaeota is a phylum of archaea belonging to the DPANN archaea. They have been discovered in acid mine drainage waters and later in marine sediments. The cells of these organisms are extremely small consistent with small genomes. Metagenomic techniques allow obtaining genomic sequences from non-cultured organisms, which were applied to determine this phylum.
Virome refers to the assemblage of viruses that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem, organism or holobiont. The word is frequently used to describe environmental viral shotgun metagenomes. Viruses, including bacteriophages, are found in all environments, and studies of the virome have provided insights into nutrient cycling, development of immunity, and a major source of genes through lysogenic conversion. Also, the human virome has been characterized in nine organs of 31 Finnish individuals using qPCR and NGS methodologies.
DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to other archaea.
The candidate phyla radiation is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.
Marine viruses are defined by their habitat as viruses that are found in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that can only replicate inside the living cells of a host organism, because they need the replication machinery of the host to do so. They can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.
Gracilibacteria is a bacterial candidate phylum formerly known as GN02, BD1-5, or SN-2. It is part of the Candidate Phyla Radiation and the Patescibacteria group.
The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases. Information for archaea was added in 2020, along with a species classification based on average nucleotide identity. Each update incorporates new genomes as well as automated and manual curation of the taxonomy.
References
- ↑ Filee, J.; Tetart, F.; Suttle, C. A.; Krisch, H. M. (2005). "Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere". Proceedings of the National Academy of Sciences. 102 (35): 12471–12476. Bibcode:2005PNAS..10212471F. doi: 10.1073/pnas.0503404102 . ISSN 0027-8424. PMC 1194919 . PMID 16116082.
- ↑ University of Tennessee at Knoxville (25 September 2018). "Study: Microbial dark matter dominates Earth's environments". Eurekalert! (Press release). Retrieved 26 September 2018.
- ↑ Rinke, Christian (2018). "Single-Cell Genomics of Microbial Dark Matter". In Robert G. Beiko; Will Hsiao; John Parkinson (eds.). Microbiome Analysis: Methods and Protocols. Methods in Molecular Biology. Vol. 1849. New York: Springer New York. pp. 99–111. doi:10.1007/978-1-4939-8728-3_7. ISBN 978-1-4939-8728-3. PMID 30298250.
- ↑ Jiao, Jian-Yu; Liu, Lan; Hua, Zheng-Shuang; Fang, Bao-Zhu; Zhou, En-Min; Salam, Nimaichand; Hedlund, Brian P; Li, Wen-Jun (2021-03-01). "Microbial dark matter coming to light: challenges and opportunities". National Science Review. 8 (3): –280. doi:10.1093/nsr/nwaa280. ISSN 2095-5138. PMC 8288357 . PMID 34691599.
- ↑ Hedlund, Brian P.; Dodsworth, Jeremy A.; Murugapiran, Senthil K.; Rinke, Christian; Woyke, Tanja (2014). "Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter"". Extremophiles. 18 (5): 865–875. doi:10.1007/s00792-014-0664-7. ISSN 1431-0651. PMID 25113821. S2CID 16888890.
- ↑ Rinke, Christian; et, al. (2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–437. Bibcode:2013Natur.499..431R. doi: 10.1038/nature12352 . hdl: 10453/27467 . PMID 23851394. S2CID 4394530.
- ↑ Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (March 2011). "Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees". PLOS ONE. 6 (3): e18011. Bibcode:2011PLoSO...618011W. doi: 10.1371/journal.pone.0018011 . PMC 3060911 . PMID 21437252.
- Colin Barras (18 March 2011). "Biology's 'dark matter' hints at fourth domain of life" . New Scientist.
- ↑ Lopez P, Halary S, Bapteste E (October 2015). "Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life". Biology Direct. 10: 64. doi: 10.1186/s13062-015-0092-3 . PMC 4624368 . PMID 26502935.
- Colin Barras (11 November 2015). "Mystery microbes in our gut could be a whole new form of life" . New Scientist.
- ↑ Schulze-Makuch, Dirk (Feb 28, 2017). "Could Alien Life Be Hidden All Around Us?". Smithsonian Magazine. Smithsonian Institution . Retrieved Nov 30, 2023.