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Techniques used to study microbe gene expression
Metatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments, i.e., the metatranscriptome. While
Metatranscriptomics
Study of genes found in the environment
in situ metatranscriptomic studies of microbial communities to date. While originally limited to microarray technology, metatranscriptomics studies have
Metagenomics
Phylogenetic group described in January 2024
phylogenetic group", as their RNA sequences, discovered by computer-aided metatranscriptomics, are not homologous with the genomic sequence of any other life form
Obelisk_(biology)
Pathogenic small single-stranded circular RNA
whose respective economic importance to humans varies widely. A 2023 metatranscriptomics study suggests that viroids and viroid-like elements can be found
Viroid
Infectious disease caused by Borrelia bacteria, spread by ticks
C, Banks PB, Michie M, Roy-Dufresne E, et al. (September 2022). "Metatranscriptomic profiling reveals diverse tick-borne bacteria, protozoans and viruses
Lyme_disease
Microbiome multi-omics bioinformatics tool
exists or is being added for analysis of shotgun metagenomics and metatranscriptomics data, as well as metabolomics mass spectrometry data. Development
QIIME
Community of microorganisms
entire microbial communities in the disciplines of metagenomics and metatranscriptomics databases accessible to researchers across multiple disciplines methods
Microbiota
DNA sampled from the environment rather than directly from an individual organism
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
Environmental_DNA
Realm of viruses
discovered to be included in the realm, but in the 2020s metagenomic and metatranscriptomic studies have discovered many prokaryotic RNA viruses. Many of the
Riboviria
Biochemical signaling between the gastrointestinal tract and the central nervous system
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Gut–brain_axis
Order of viruses
Insthoviricetes. The order contains two families and eight genera. Metatranscriptomics of aquatic animal samples paired with phylogenetics suggests that
Articulavirales
Species of virus
influenza A virus are estimated to have diverged 2,000 years ago. Metatranscriptomics studies have also identified closely related "influenza B-like" viruses
Influenza_B_virus
Korean side dish of fermented vegetables
Hyun Mi; Hahn, Yoonsoo; Madsen, Eugene L.; Jeon, Che Ok (2013). "Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation"
Kimchi
Process of determining the nucleic acid sequence
Library Preparation Methods Reveals Their Impact on Interpretation of Metatranscriptomic Data". BMC Genomics. 15 (1): 912–12. doi:10.1186/1471-2164-15-912
DNA_sequencing
Microbial community assemblage and activity
of functional genes, metagenomics) to analyze microbial activity (metatranscriptomics, metaproteomics, metabolomics). Based on metagenome data, microbial
Microbiome
Marine flowering plants
Wojahn, John M.; Tomas, Fiona; Mueller, Ryan S. (15 March 2018). "Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes"
Seagrass
Method of species identification using a short section of DNA
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
DNA_barcoding
Tiny lifeforms floating and drifting in the air, carried by the wind
technologies, such as metabarcoding as well as coordinated metagenomics and metatranscriptomics studies, have been providing new insights into microbial ecosystem
Aeroplankton
Scientific study of chemical processes involving metabolites
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Metabolomics
Antarctica's largest known subglacial lake
response". Nature. doi:10.1038/nature.2013.13364. Gura, Colby (2020). "Metatranscriptomic and Metagenomic Analysis of Biological Diversity in Subglacial Lake
Lake_Vostok
Region of soil or substrate comprising the root microbiome
microbial community composition and diversity. Metagenomics and Metatranscriptomics: Shotgun sequencing of total DNA or RNA to assess the genetic potential
Rhizosphere
Genetic testing technique
single cell and population genome recovery". Microbial Metagenomics, Metatranscriptomics, and Metaproteomics. Methods in Enzymology. Vol. 531. pp. 3–19. doi:10
Fluorescence in situ hybridization
Fluorescence_in_situ_hybridization
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Poultry_microbiome
Endosymbiotic bacterium or fungus
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Endophyte
Host and associated species living as a discrete ecological unit
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Holobiont
Accumulation of brine in a seafloor depression
tracking. Other DHABs have been analyzed for anammox pathways using metatranscriptomic techniques with little positive results, which may be due to the limitations
Brine_pool
Microorganisms in or on human skin and biofluids
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Human_microbiome
Genetic technique for identifying organisms in mixed samples
"who" is present, while the function of communities or individuals can be established using a metagenomics, single‐cell genomics or metatranscriptomics.
Metabarcoding
Family of viruses in the order Nidovirales
Benjamin W. (2018-11-01). "Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae
Coronaviridae
Identification of fungal species thanks to specific DNA sequences
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
Fungal_DNA_barcoding
Species of virus
to have diverged from a common ancestor around 8,000 years ago. Metatranscriptomics studies have also identified closely related "Influenza C and D-like"
Influenza_D_virus
Group of bacteria affecting plant growth
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Rhizobacteria
Community of microorganisms found in or around sponges
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Sponge_microbiomes
Group of viruses associated with bats
and biological confirmation of a highly divergent Tacaribe virus in metatranscriptomic data from neotropical bats". mSphere. 9 (10) e00520-24. doi:10.1128/msphere
Bat_virome
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
Fish_DNA_barcoding
Aspect of DNA testing
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
Microbial_DNA_barcoding
Total collection of viruses in and on the human body
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Human_virome
Open-Source Workflow Management Platform
Eduardo; Andrés-León, Eduardo (2022). "Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice". Genes. 13 (12): 2280
Nextflow
Software for understanding biological data
plays an important role in microbial interaction. Metagenomic and metatranscriptomic data are an important source for deciphering communications signals
Machine learning in bioinformatics
Machine_learning_in_bioinformatics
Region of soil surrounding a germinating seed
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Spermosphere
Phylum of fungi
before amplification through the polymerase chain reaction (PCR). A metatranscriptomic survey of the Sevilleta Arid Lands found that 5.4% of the fungal rRNA
Glomeromycota
Separation of a strain from a mixed population of microbes
methods (particularly environmental or soil bacteria) metagenomics or metatranscriptomics are used, shotgun sequencing or PCR directed sequencing of the genome
Isolation_(microbiology)
Examines sequence information from individual cells
microbiomes. It would address issues encountered in conventional bulk metatranscriptomics approaches, such as failing to capture species present in low abundance
Single-cell_sequencing
Fungal community in and on an organism
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Mycobiome
Plant surfaces as habitats for microorganisms
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Phyllosphere
Genus of eukaryotic microbes
indexes extensive nucleotide content, searching for metagenomic and metatranscriptomic matches in the databases. This located a few matches sparsely distributed
Solarion
Technique used for species identification and phylogenetic studies
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
Algae_DNA_barcoding
PMC 2268829. PMID 18316740. ">Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column"
IMES-4_RNA_motif
Any life form too small for the naked human eye to see that lives in a marine environment
of the host-microbiome interactions. For instance, metagenomics, metatranscriptomics, metaproteomics and metabolomics methods are all used to provide
Marine_microorganisms
Genus of protists
biological and pathological features are currently unknown. Through metatranscriptomics using RNA-seq technology combined with field-emission microscopy
Neobodo
Marine community of plankton and microbes
is fairly limited, monitoring for changes using metagenomics and metatranscriptomics is a promising field that may provide more insight and predictions
Phytoplankton_microbiome
Process of identifying pollen donor plant species
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
Pollen_DNA_barcoding
deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics". The ISME Journal. 13 (8): 2044–2057. Bibcode:2019ISMEJ..13.2044T
Acidulidesulfobacteriota
Genus of viruses in the family Orthomyxoviridae
six lineages, which were estimated to have emerged around 1896 AD.Metatranscriptomics studies also have identified closely related "Influenza C and D-like"
Influenza_C_virus
Cooperation between microbial species to digest a substrate
bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics". The ISME Journal. 14 (4): 906–918. Bibcode:2020ISMEJ..14..906H
Syntrophy
Former research initiative
profiling, whole metagenome shotgun sequencing, whole genome sequencing, metatranscriptomics, metabolomics/lipidomics, and immunoproteomics. The key findings
Human_Microbiome_Project
PMC 2704228. PMID 19531245. Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column"
RNAs present in environmental samples
RNAs_present_in_environmental_samples
Microorganisms living in the fruit fly
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Microbiome in the Drosophila gut
Microbiome_in_the_Drosophila_gut
Use of DNA barcoding to analyse the diet of organisms
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
DNA barcoding in diet assessment
DNA_barcoding_in_diet_assessment
American microbiologist (born 1958)
PMID 26042105. Shi, Yanmei; Tyson, Gene W.; DeLong, Edward F. (2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column"
Edward_DeLong
derived from metagenomic samples. While untargeted metagenomics and metatranscriptomics does not need a genetic marker, amplicon sequencing does. It uses
Viral_metagenomics
Microbe community of plant roots
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Root_microbiome
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Plant_holobiont
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Marine_holobiont
Microscale mucus region that is rich in organic matter surrounding a phytoplankton cel
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Phycosphere
Study of interactions between Earth and the biosphere
Searching for similar genes in other organisms and in metagenomic and metatranscriptomic data allows us to understand what processes could be relevant and
Geobiology
PMC 4140389. PMID 19956260. Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column"
IMES-3_RNA_motif
Species of sponge
Christoph; Rapp, Hans Tore; Urich, Tim; Schleper, Christa (2012-05-01). "Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function
Geodia_barretti
Collection of viruses in an organism or ecosystem
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Virome
Study of all proteins in an environment
environmental studies involving potentially harmful contaminants. Metatranscriptomics Dill BD, et al. (2010). "Metaproteomics: Techniques and Applications"
Metaproteomics
Biological kingdom of archaea
S2CID 26033384. Murakami S, Fujishima K, Tomita M, Kanai A (February 2012). "Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals
Nanobdellati
Microbiological non-culture dependent methods
De-Chen; Shi, Ming-Jing; Chen, Guan-Jun; Du, Zong-Jun (2018-12-26). "Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during
Microbial_dark_matter
Species of bacterium
lifestyle' of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community
Clostridium_scindens
Community of microorganisms found in or around specific marine environments
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Marine_microbiome
Genus of viruses
(7 September 2018). "Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae
Alphaabyssovirus
Study of the interaction of soil and life
environmental DNA. Various omics approaches, such as metagenomics, metatranscriptomics, proteomics and proteogenomics, are rapidly advancing, at least for
Soil_ecology
Incredibly small, unique extremophile Archaea species found deep in an acidic mine
life in the extreme Río Tinto, ISME Journal 2010 Murakami et al. Metatranscriptomic analysis of microbes in an ocean-front deep subsurface hot spring
Archaeal Richmond Mine acidophilic nanoorganisms
Archaeal_Richmond_Mine_acidophilic_nanoorganisms
of high-performance computing for annotating data. Metagenomic and metatranscriptomic studies involve the processing of large datasets, and therefore they
MG-RAST
Assembly of microorganisms near plants
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Plant_microbiome
Technique used in macroinvertebrate biology
Environmental DNA (eDNA) environmental RNA Metagenomics viruses Metatranscriptomics Amplification PCR Shotgun sequencing High throughput sequencing Extracellular
Aquatic macroinvertebrate DNA barcoding
Aquatic_macroinvertebrate_DNA_barcoding
American bacteriologist
occurring in the ocean, she uses ecological genomics, metagenomics and metatranscriptomics to study the genes and activity of marine bacteria in nature. As
Mary_Ann_Moran
program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. The core algorithm is based on approximate seeds
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Group of communities of microorganisms that reside within whales
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Cetacean_microbiome
PMC 4140389. PMID 19956260. Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column"
IMES-2_RNA_motif
Species of rodent
Yu, Qiaoling; Han, Qian; Qu, Jiapeng; Li, Huan (15 April 2025). "Metatranscriptomics reveals that plant tannins regulate the expression of intestinal
Plateau_vole
RNA family
PMC 4140389. PMID 19956260. Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column"
Ocean-VII_RNA_motif
Genus of archaea
Trevor L.; Lovley, Derek R. (2017). Schloss, Patrick D. (ed.). "Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter
Methanothrix
PMC 4140389. PMID 19956260. Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column"
IMES-1_RNA_motif
Mountain in Oklahoma, United States
Elshahed, Mostafa S.; Najar, Fares Z.; Krumholz, Lee R. (2015-09-22). "Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur
Zodletone_Mountain
Species of bacterium
Martin HG, Ivanova N, Rohwer F, Hugenholtz P, McMahon KD (2010). "Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched
Accumulibacter_phosphatis
Microbial population biology Microbial cooperation Metagenomics viral Metatranscriptomics Metabolomics Pan-genome Superorganism Symbiogenesis Projects Human
Marine_microbial_symbiosis
Species of amphibian
Benjamin W. (2018). "Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae
Microhyla_fissipes
American scientist and academic
expression, chromatin accessibility, proteomic, metagenomic, and metatranscriptomic assays. This collection of data was made public in NASA's Open Science
Eliah_G._Overbey
Species of bacterium
Haruta, S.; Nishihara, A.; Hanada, S.; Thiel, V. (2021). "In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic
Chloroflexus_aggregans
Major circulating ecosystem of ocean currents
A. E.; Zehr, J. P.; Moran, M. A. (2009). "Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical
Ecosystem of the North Pacific Subtropical Gyre
Ecosystem_of_the_North_Pacific_Subtropical_Gyre
German microbiologist
combines ecological field studies with modern genomic, metagenomic, and metatranscriptomic approaches as well as bioinformatic analyses. In this context, the
Rudolf_Amann
Species of lichen-forming fungus
Helen; Harley, Joanna; Bird, Kimberley; Cunliffe, Michael (2024). "Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon
Lichina_pygmaea
Community of plants (phyto) situated in their specific ecological areas (biome)
of organisms across every kingdom of life. Recent metagenomic and metatranscriptomic approaches have allowed scientists to discover novel taxonomic species
Phytobiome
Family of viruses
decreases in prawn production of more than 50% in some cases. Through metatranscriptomic sequencing of the viromes of healthy prawns and prawns with GRD, and
Marnaviridae
METATRANSCRIPTOMICS
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Surname or Lastname
English (Lancashire)
English (Lancashire) : habitational name from a place called Dugdale, probably the hamlet near Uttoxeter, Staffordshire, now known as Dagdale, from the Old English personal name or byname Ducca + Old English dæl or Old Norse dalr ‘valley’.
Girl/Female
Australian, British, Celtic, English, Irish
Life
Boy/Male
British, English
Highborn Friend
Girl/Female
Hindu
Retribution
Boy/Male
Egyptian Muslim
He shall add.
Female
Persian/Iranian
(يسمن) Persian form of Arabic Yasmin, YASAMIN means "jasmine flower," a plant in the olive family.
Female
Welsh
Welsh unisex form of German Emmeline, EMLYN means "work."
Girl/Female
Indian
Flame, Light, Shinning
Boy/Male
Tamil
One who bestows peace, Name of a himalayan peak, Abode of Shiva
Boy/Male
Hindu, Indian, Tamil
Benevolent
METATRANSCRIPTOMICS
METATRANSCRIPTOMICS
METATRANSCRIPTOMICS
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METATRANSCRIPTOMICS