№ lp_2_3_43085
File format: docx
Character count: 14353
File size: 168 KB
List of OTUs identified in gut contents of three fish species with sequence counts, taxonomic assignment, and reference accession numbers.
Year:
2009
Source type:
Scientific appendix
Subject:
Fish diet analysis, gut content metabarcoding
Organism focus:
Paracirrhites arcatus, Neocirrhites armatus, Caracanthus maculatus
Data type:
OTU table with sequence counts
Method:
DNA sequencing, BLASTn, Bayesian assignment
References:
Machida et al., 2009; Plaisance et al., 2009
Additional resources:
BIOCODE reference specimens (http://biocode.berkeley.edu
Note:
)
Taxonomic groups:
Polychaeta, Malacostraca, Maxillopoda
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Document type:
Supplementary scientific data table
Subject area:
Microbiology; Marine biology; Microbial ecology
Biological subject:
Brisaster townsendi
Data type:
OTU abundance counts and taxonomic identification
Taxonomic ranks included:
Phylum; lowest taxonomic level
Sample source:
Digestive tract of Brisaster townsendi
Sample sections:
Stomach; Intestine; Intestinal caecum; Rectum
Number of stomach samples:
2
Number of intestine samples:
2
Number of intestinal caecum samples:
12
Number of rectum samples:
2
Minimum sequence threshold:
2,000 sequences per OTU
Measured variable:
Sequence abundance per OTU across digestive tract compartments
Taxonomic groups represented:
Bacteroidetes; Deltaproteobacteria; Gammaproteobacteria; Alphaproteobacteria; Epsilonproteobacteria; Patescibacteria; Spirochaetes; Unassigned
Identifiers used:
Operational Taxonomic Unit (OTU) numbers
Year:
2023
Region / City:
California, USA
Topic:
Organic Waste Management, SB 1383 Regulations
Document Type:
Policy Model
Agency / Organization:
CalRecycle, HF&H Consultants, Debra Kaufman Consulting
Author:
CalRecycle, HF&H Consultants, Debra Kaufman Consulting
Target Audience:
Jurisdictions, regulatory bodies, waste management authorities
Effective Date:
January 1, 2022
Amendments Date:
June 15, 2023
Year:
2018, 2019
Region:
Oklahoma
Topic:
Bacterial spot disease on tomato
Document type:
Research article
Institution:
Not specified
Author:
Not specified
Target audience:
Researchers, plant pathologists
Period of validity:
Not specified
Approval date:
Not specified
Date of amendments:
Not specified
Year:
1995
Region / city:
Florida, USA
Topic:
Environmental regulations
Document type:
Legal/Regulatory
Organization:
Florida Department of Environmental Protection
Author:
Florida Department of Environmental Protection
Target audience:
Individuals and businesses handling recovered materials or post-use polymers
Period of validity:
Ongoing since 1995
Approval date:
1995-01-01
Amendment date:
2013-12-17
Year:
2019
Region / city:
United Kingdom
Topic:
Health and Safety, Machinery Procurement, Industrial Equipment
Document Type:
Procedure
Organization / Institution:
PABIAC
Author:
PABIAC, Health and Safety Executive
Target Audience:
Industry professionals involved in the procurement of machinery, plant, and equipment
Effective Period:
Ongoing
Approval Date:
September 2019
Modification Date:
Not specified
Year:
2019
Region / city:
Not specified
Theme:
Taxonomy
Document type:
Proposal
Organization / institution:
ICTV
Author:
Kropinski AM, Adriaenssens EM
Target audience:
ICTV Subcommittee Chair, virus taxonomy specialists
Period of validity:
Not specified
Approval date:
Not specified
Date of revisions:
Not specified
Journal:
Microbial Ecology
Article title:
Taxonomic dependency of beta diversity for bacteria, archaea and fungi in a semi-arid lake
Authors:
Haijun Yuan; Weizhen Zhang; Huaqun Yin; Runyu Zhang; Jianjun Wang
Corresponding author:
Jianjun Wang ([email protected]
Note:
)
Affiliations:
State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China; University of Chinese Academy of Sciences, Beijing, China; School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
Study area:
Hulun Lake, China
Subject:
Microbial ecology; beta diversity; environmental gradients
Microbial groups:
Bacteria; Archaea; Fungi
Environmental factors:
Water physicochemical variables; Sediment properties
Statistical analyses:
Pearson correlation; Mantel test; Spearman correlation; Linear and quadratic models
Content:
Supplementary tables and figures (Table S1–S2; Fig. S1–S4)
Year:
2018
Region / City:
Guelph, Liverpool
Subject:
Taxonomy
Document Type:
Taxonomic Proposal
Organization:
ICTV
Author:
Andrew M. Kropinski, Evelien Adriaenssens
Target Audience:
ICTV Subcommittee Members, Researchers in Viral Taxonomy
Period of Validity:
N/A
Approval Date:
March 2018
Date of Revision:
N/A
Document type:
Supplementary scientific data table
Subject area:
Microbiology; Marine biology; Microbial ecology
Biological subject:
Brisaster townsendi
Data type:
OTU abundance counts and taxonomic identification
Taxonomic ranks included:
Phylum; lowest taxonomic level
Sample source:
Digestive tract of Brisaster townsendi
Sample sections:
Stomach; Intestine; Intestinal caecum; Rectum
Number of stomach samples:
2
Number of intestine samples:
2
Number of intestinal caecum samples:
12
Number of rectum samples:
2
Minimum sequence threshold:
2,000 sequences per OTU
Measured variable:
Sequence abundance per OTU across digestive tract compartments
Taxonomic groups represented:
Bacteroidetes; Deltaproteobacteria; Gammaproteobacteria; Alphaproteobacteria; Epsilonproteobacteria; Patescibacteria; Spirochaetes; Unassigned
Identifiers used:
Operational Taxonomic Unit (OTU) numbers
Year:
2023
Region:
Brazilian Atlantic Forest, South America
Topic:
Biodiversity conservation, freshwater turtles
Document type:
Supplementary data appendix
Institution:
Universidade Federal do Rio de Janeiro
Authors:
Rhodin et al., Vogt et al., Bernils et al.
Species covered:
Chelonoidis carbonarius, Chelonoidis denticulatus, Kinosternon scorpioides, Rhinoclemmys punctularia, Trachemys dorbigni, Acanthochelys radiolata, Acanthochelys spixii, Hydromedusa maximiliani, Hydromedusa tectifera, Mesoclemmys hogei, Mesoclemmys tuberculata, Mesoclemmys vanderhaegei, Phrynops geoffroanus, Phrynops hilarii, Phrynops williamsi
Functional traits analyzed:
Body size, habit, activity, diet, environment, habitat
Data sources:
Published literature and species distribution records
Geographic details:
Brazilian states including RS, SC, PR, MS, SP, GO, MG, RJ, ES, BA, SE, AL, PE, PB, RN; Serra do Mar, Serra da Mantiqueira, Central Corredor, Pernambuco Endemism Center
Tables included:
Species distribution, functional traits, ecosystem functions
Figures included:
Original distribution of Brazilian Atlantic Forest hotspot
References:
Junk 1997; Van Dijk et al. 2014; Vitt and Caldwell 2014; Sobral-Sousa et al. 2017; Staford et al. 2018; additional primary sources for species data
Year:
2023
Methodology:
In silico simulation of species identification
Technology:
Illumina HiSeq 2000
Sequencing strategy:
100 bp paired-end (PE) shotgun reads
Reference library:
COI barcode library (when available)
Assembly software:
SOAPdenovo
Taxonomic scope:
Insect mitochondrial genomes
Sample type:
Mock-up pooled insect communities
Species tested:
209 complete mitochondrial genomes
Analysis depth:
100X and 1,000X sequencing coverage
Objective:
Comparison of reference-based and reference-independent taxonomic identification methods
Key variables:
Relatedness of species, abundance, sequencing depth, barcode length
Validation:
Alignment criteria >99% identity, coverage >90% for reference detection
Year:
2025
Region / City:
Global
Theme:
Taxonomy, Virology
Document type:
Guidelines
Organization / Institution:
ICTV
Author:
ICTV
Target audience:
Virologists, Taxonomists, ICTV members
Period of validity:
Ongoing
Approval date:
Not specified
Date of amendments:
Not specified