Category talk:Pages with missing NCBI ID

From BugSigDB

Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in resolving all missing NCBI IDs in a signature, the signature will disappear from that page. See https://en.wikipedia.org/wiki/Open_nomenclature for help with nomenclature conventions, and use the NCBI Taxonomy Browser. Here is a 2-hour video of Levi working on mapping to the NCBI taxonomy.

Some useful nomenclature[edit]

Nomenclature found in taxa reported in the literature
Nomenclature Meaning Example How to resolve Link for more info
UCG Uncultured genus-level group Ruminococcaceae UCG-014 sp This example can be treated as an uncultured Ruminococcaceae bacterium, which is listed in NCBI under a heterotypic synonym uncultured Oscillospiraceae bacterium. This is good because it has the correct rank (species) and identifies the finest-known level of taxonomy (family Oscillospiraceae / Ruminococcaceae) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407505/
Incertae sedis or problematica Latin for 'of uncertain placement' I decided to call the Gemellaceae family Bacilli incertae sedis because references to it were usually under the Bacilli class but otherwise uncertain a term used for a taxonomic group where its broader relationships are unknown or undefined. https://en.wikipedia.org/wiki/Incertae_sedis
Example Example Example Example Example

changed Ruminococcaceae UCG-014 to uncultured Oscillospiraceae bacterium[edit]

Uncultured Ruminococcaceae bacterium is its heterotypic synonym in NCBI and as stated in the table above.--Joan Chuks (talk) 16:11, 10 March 2024 (UTC) The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness/Experiment 5/Signature 1 and The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness/Experiment 6/Signature 1--Joan Chuks (talk) 15:32, 13 March 2024 (UTC) https://bugsigdb.org/Study_961/Experiment_1/Signature_2 Changed unidentified Ruminococcacea to unclassified Oscillospiraceae. Unclassified Oscillospiraceae is a heterotypic synonym to unclassified Ruminococcaceae

Unresolved nomenclature existing in bugsigdb.org[edit]

Signatures from the top of the list until this signature have been previously investigated but remain unsolved:

  • Association Between Gut Microbiota and Helicobacter pylori-Related Gastric Lesions in a High-Risk Population of Gastric Cancer/Experiment 4/Signature 1

The following signatures have unmapped taxa that someone has looked into but been unable to resolve:

Paraprevotellaceae family[edit]

The order Bacteroidales, which is part of the phylum Bacteroidetes, is home to the Paraprevotellaceae family of bacteria. These bacteria are widespread in the human gut microbiota and aid in the fermentation of complex carbohydrates like dietary fiber. They are anaerobic microbes, which means they flourish in oxygen-free environments.

Among the bacteria in the family Paraprevotellaceae are the genera Paraprevotella, Alloprevotella, and Ezakiella. These bacteria are currently being studied, and their particular roles and functions within the gut microbiome are unknown......Adanwa

Mogibacteriaceae family[edit]

The Mogibacteriaceae family is a phylum Bacteroidetes family of bacteria. These bacteria are found in the human microbiome, namely in the oral microbiota. Mogibacterium is one of several genera of the Mogibacteriaceae family, with Mogibacterium being the most well-known.

Mogibacterium and related bacteria can be discovered in a variety of human oral locales, including dental plaques, saliva, and the oral mucosa. They are anaerobic bacteria, which means they flourish in oxygen-free settings.

The Mogibacteriaceae family is currently being studied, and its specific roles and functions in the oral microbiome are still being investigated. The oral microbiota is complex and diverse, with various interactions and consequences on oral health and disorders such as dental caries and periodontal disease.

Anaerovoracaceae is shown in LPSN: as a heterotypic synonym for Mogibacteriaceae family (Chuvochina et al. 2024) and validly published under the ICNP.

couldn't find order gemellales[edit]

couldn't find ASV_209 (Clostridia), ASV_157 (Absconditabacteria), ASV_205 (Clostridia), ASV-62 (Lachnospiraceae), (F0058 (Paludibacteria)[edit]

"SMB53" family in order Clostridiaceae[edit]

family Dehalobacteriaceae[edit]

Findings from List of Prokaryotic names with Standing in Nomenclature (LPSN) shows the correct name for family Dehalobacteriaceae to be Peptococcaceae Rogosa 1971 (Approved Lists 1980)--Joan Chuks (talk) 14:46, 24 April 2024 (UTC)

Clostridia clusters IV, XIVa, and XVIII[edit]


=== Clostridium IV and Clostridium XIVb

  • [1] Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls/Experiment 1/Signature 2

Clostridium IV is changed to Ruminococcaceae Clostridium XIVb is changed to Lachnospiraceae according to [2] (Omojokun)

"Clostridia group xiv, Clostridium_XlVb, Clostridium_IV, Clostridium_XlVa "[edit]

"RsaHF231" "SHA-109"[edit]

family ruminococcaceae[edit]

Experiment_1/Signature_1[edit]

Lachnospiraceae_NK4A136 was updated to Lachnospiraceae bacterium NK4A136

uncultured Erysipelotrichaceae bacterium[edit]

Gut microbiome signatures reflect different subtypes of irritable bowel syndrome Erysipelotrichaceae_ucg_003 was updated to uncultured Erysipelotrichaceae bacterium (taxID, 331630) in experiments 1,2 and 3 (ChiomaOnyido)

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans/Experiment 3/Signature 2 Erysipelotrichaceae UCG 003 was updated to Uncultured Erysipelotrichaceae bacterium (NCBI ID -331630)--Joan Chuks (talk) 16:44, 10 March 2024 (UTC)

Uncultured genus DSSF69[edit]

From google searches, this appears to be an uncultured genus within the Sphingomonadaceae family, in class alphaproteobacteria...(Esther Afuape)

Lachnoclostridium lactaris[edit]

Seems like Ruminococcus lactaris but I'm not sure as the latter does not belong to genus Lachnoclostridium. I replaced it with Uncultured Lachnoclostridium sp. with taxID 1586779 which is a good fit as it has the correct rank of species...(Esther Afuape )

Possible taxonomy lineage of TG5[edit]

Kingdom -Bacteria; Phylum - Synergistota; class - Synergistia; Order -Synergistales, Family-Dethiosulfovibrionaceae Source: Pub med central article--Joan Chuks (talk) 01:36, 2 April 2024 (UTC)

Lachnoclostridium faecis[edit]

Lachnoclostridium faecis was replaced with Lachnoclostridium sp. (Taxonomy ID: 2028282). This is a likely good fit as it has the correct rank of species and falls under the genus "unclassified Lachnoclostridium"--Joan Chuks (talk) 12:11, 2 April 2024 (UTC)

Marinicellaceae Family[edit]

The Marinicellaceae family belongs to the phylum Pseudomonadota and class Gammaproteobacteria...(Victoria)

The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels[edit]

https://bugsigdb.org/Talk:Study_911 contains record of https://bugsigdb.org/Study_911 unresolved Taxa --Joan Chuks (talk) 07:56, 27 March 2024 (UTC)

tricky but solved[edit]

Changed Bacillus (Priestia) megaterium to Priestia megaterium Synonyms Bacillus megaterium[edit]

This was tricky but I think it's right.

  • Microbial communities associated with honey bees in Brazil and in the United States/Experiment 1/Signature 1

Changed Bacillus (Priestia) aryabhattai to Priestia aryabhattai Synonyms Bacillus aryabhattai[edit]

This was tricky but I think it's right.

  • Microbial communities associated with honey bees in Brazil and in the United States/Experiment 1/Signature 1

Changed Acetobacterales order to Rhodospirillales order[edit]

This was tricky but I think it's right.

Changed Pseudopropionibacterium to Arachnia[edit]

..(Chinelsy)

Changed unknown proteobacterium to unidentified proteobacterium[edit]

Changed unknown bacteria to bacterium[edit]

Changed Brevibacterium massiliense to Brevibacterium ravenspurgense[edit]

Changed Erysipelatoclostridium to Thomasclavelia[edit]

Changed unknown Actinomycetales to uncultured actinomycete[edit]

Changed Cyanobacteria to Cyanobacteriota[edit]

Changed Proteobacteria to Pseudomonadota[edit]

  • e.g. https://bugsigdb.org/Study_799/Experiment_2/Signature_2, gave it Taxonomy ID: 1224 since proteobacteria is BLAST name to current name Pseudomonadota ..(Chinelsy), [3] [Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode]..(Ayibatari),

[4] [Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome]..(Rahila) [5] [Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome]..(Rahila)

https://bugsigdb.org/Study_927/Experiment_2/Signature_2, gave it Taxonomy ID: 1224 since proteobacteria is BLAST name to current name Pseudomonadota found in ( https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1224&mode=info )(omojokun)

Changed unclassified Proteobacteria to unclassified Pseudomonadota[edit]

Changed Enterobacteriales to Enterobacterales[edit]

gave it Taxonomy ID: 91347 since Enterobacterales is heterotypic synonym to Enterobacteriales, [Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome]..(Rahila)

Changed Prevotella stercorea to Leyella stercorea[edit]

gave it Taxonomy ID: 363265 since Leyella stercorea is basionym to Prevotella stercorea, [Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome]..(Rahila)

Changed Prevotella stercorea CAG:629 to Leyella stercorea CAG:629[edit]

gave it Taxonomy ID: 1263103 since Leyella stercorea CAG:629 is homotypic synonym to Prevotella stercorea CAG:629, [Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome]..(Rahila)

Changed Verrucomicrobia to Verrucomicrobiota[edit]

Changed Clostridiales to Eubacteriales[edit]

e.g https://bugsigdb.org/Study_956/Experiment_1/Signature_1 the clostridiales should be changed to Eubacterium nodatum (Clostridiales) according to this website https://www.sciencedirect.com/topics/medicine-and-dentistry/clostridiales. (0mojokun)

Changed Lactobacillus rhamnosus to Lacticaseibacillus rhamnosus[edit]

  • e.g. https://bugsigdb.org/Study_932/Experiment_7/Signature_1, gave it Taxonomy ID: 47715 since Lacticaseibacillus rhamnosus is homotypic synonym to Lactobacillus rhamnosus [Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode]..(Ayibatari)

Changed Dialister sp. Marseille-P5638 to Dialister massiliensis[edit]

  • e.g. https://bugsigdb.org/Study_932/Experiment_1/Signature_2, gave it Taxonomy ID: 2161821 since Dialister massiliensis is current name of Dialister sp. Marseille-P5638 [Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode]..(Ayibatari)

Changed Actinobacteria to Actinomycetota[edit]

  • e.g. https://bugsigdb.org/Study_932/Experiment_6/Signature_1, gave it Taxonomy ID: 201174 since Actinomycetota is equivalent of Actinobacteria [Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode]..(Ayibatari),[6][Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome]..(Rahila)

Changed Lactobacillus fermentum to Limosilactobacillus fermentum[edit]

  • e.g. https://bugsigdb.org/Study_932/Experiment_6/Signature_1, gave it Taxonomy ID: 1613 since Limosilactobacillus fermentum is the current name of Lactobacillus fermentum [Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode]..(Ayibatari)

Changed Corynebacteriales to Mycobacteriales[edit]

  • e.g. https://bugsigdb.org/Study_932/Experiment_6/Signature_1, gave it Taxonomy ID: 85007 since Mycobacteriales is the homotypic synonym of Corynebacteriales [Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode]..(Ayibatari)

Changed Bifidobacterium kashiwanohense to Bifidobacterium catenulatum subsp. kashiwanohense[edit]

Changed Catabacter to Christensenella[edit]

Changed unclassified Ruminococcaceae to unclassified Oscillospiraceae[edit]

changed TM7a to unclassified Candidatus Saccharibacteria[edit]

Gave it Taxonomy ID: 1895827. The genus was reported as TM7a. On researching, I found that "unclassified Candidatus Saccharibacteria" has Rank: no rank.

Changed Synergistetes to Synergistota[edit]

Changed Lactobacillus mucosae to Limosilactobacillus mucosae[edit]

=== Changed Bacteroides sp. NSJ-2 to Bacteroides hominis (ex Liu et al. 2022)

Changed Prevotella timonensis to Hoylesella timonensis[edit]

Changed Actinomyces turicensis to Schaalia turicensis[edit]

Changed Propionicibacterium lymphophilum to Propionimicrobium lymphophilum[edit]

Changed Facklamia ignava to Falseniella ignava[edit]

Changed Actinomyces neuii to Winkia neuii[edit]

Changed Atopobium vaginae to Fannyhessea vaginae[edit]

Changed Lactobacillus vaginalis to Limosilactobacillus vaginalis[edit]

Changed Campylobacteria to Epsilonproteobacteria[edit]

Changed Enterobacteriales to Enterobacterales[edit]

"candidatus" genus[edit]

Changed Leuconostocaceae to Lactobacillaceae[edit]

..(Chinelsy)

Changed Eubacterium_brachy_group to [Eubacterium] brachy[edit]

..(Chinelsy)

“MITOCHONDRIA” cellular organelle[edit]

  • e.g. https://bugsigdb.org/Study_509/Experiment_2/Signature_2, removed “mitochondria” which was described as an organism (bacteria) and cannot be rather They are often referred to as the "powerhouses of the cell" because they are responsible for producing adenosine triphosphate (ATP), the primary energy currency of the cell, through a process called oxidative phosphorylation. I just removed it from this signature …(Chinelsy)

"mitochondria" was not curated because it is a cell organelle and not a bacteria...(Victoria)

"CHLOROPLAST" An Organelle[edit]

  • e.g. https://bugsigdb.org/Study_835/Experiment_6/Signature_1, removed "chloroplast" which is an organelle found in the cells of photosynthetic organisms, such as plants, algae, and some types of bacteria. Chloroplasts are responsible for the process of photosynthesis, which allows these organisms to convert light energy into chemical energy in the form of glucose or other organic compounds. I just removed it from this signature …(Chinelsy)

CHLOROPLAST[edit]

During one of the discussions in the BugSigDB community, one of the curators mapped Chloroplast to cyanobacteriota, which was confirmed by the mentors. Source: https://en.wikipedia.org/wiki/Chloroplast I agree that chloroplast should be curated as "Cyanobacteriota" and not removed... (Chioma Onyido)

"OD1"[edit]

 https://bugsigdb.org/Study_793/Experiment_1/Signature_1

Research shows that Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis...(Chinelsy)

unclassified Eubacteriales[edit]

k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39[edit]

k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__S24.7[edit]

Escherichia/Shigella sp.[edit]

Gemellaceae Family[edit]

Gemellaceae = 539738

Some were previously called Bacilli incertae sedis (NCBI ID: 112452) - would be great to fix now the ones of these that were originally Gemellaceae to 539738

Clostridia XI[edit]

Replaced "UNKNOWN" TAXA with "UNCLASSIFIED" TAXIDs[edit]

  • Replaced "unknown saccharimonadia", "unknown saccharimonadales", "unknown clostridia UCG", "unknown veillonellaceae", "unknown prevotellaceae", "unknown prevotella", "erysepylobacte", "unknown bacteroidales", "unknown bacteroidia", "unknown gracilibacteria", "unknown gammaproteobacteria" and "unknown lachnospiraceae"

with "unclassified candidatus saccharimonadia", "unclassified candidatus saccharimondales", "uncultured clostridia bacterium", "unclassified veillonellaceae", "unclassified prevotellaceae", "unclassified prevotella", "unclassified erysipelotricaceae", "unclassified bacteroidales, "unclassified bacteroidia, "unclassified candidatus gracilibacteria", "unclassified gammaproteobacteria" and "unclassified lachnospiraceae", respectively in https://bugsigdb.org/Study_799 ... (Chioma Onyido)

Changed BD1-5 (GN02) to Candidate phylum Gracilibacteria[edit]

originally reported as BD1-5 (GN02), I curated as "Candidate phylum Gracilibacteria" because Candidate phylum Gracilibacteria was formerly known as GN02, BD1-5 or SN-2 according to web sources https://bugsigdb.org/Study_678 ... (Chioma Onyido)

changed TM7 to Candidatus saccharibacteria[edit]

The phylum was reported as TM7. On reasearching, I found that "Candidatus saccharibacteria" which has the correct rank of phylum, was formerly known as TM7. This was while reviewing https://bugsigdb.org/Study_756... (Afuape Esther)

TM7 in Study-300 changed to Candidatus Saccharibacteria (Taxonomy ID: 95818) “Candidatus Saccharibacteria” was proposed as the new phylum name for TM7 based on the genomic analysis, which suggested that these bacteria, with reduced genomes, consume primarily sugar compounds. This information was found in the study, Saccharibacteria (TM7) in the Human Oral Microbiome(Sage-Journals)--Joan Chuks (talk) 01:52, 2 April 2024 (UTC)

resolved WAL 1855D[edit]

found WAL_1855D to be Sporobacterium sp. WAL 1855D with NCBI ID 507843. It has the correct rank of species. It appeared in https://bugsigdb.org/Study_776... (Afuape Esther)

WAL_1855D updated to Sporobacterium sp. WAL 1855D (tx id - 507843)in https://bugsigdb.org/Study_803 --Joan Chuks (talk) 17:19, 2 April 2024 (UTC)

resolved Bacteria_p_OD1[edit]

found Bacteria_p_OD1 to be Candidatus Parcubacteria with NCBI ID 221216. It has the correct rank of phylum and appeared in study https://bugsigdb.org/Study_793... (Afuape Esther)

unclassified Rhodobacteriaceae[edit]

un_Rhodobacteraceae: found as unclassified Paracoccaceae...(Esther Afuape)

TG5[edit]

found TG5 to be unclassified Synergistales with the Tax ID 1151719. It appeared in the study https://bugsigdb.org/Study_157/Experiment_2/Signature_2 ... (Eniola Adebayo)

unclassified bacteria[edit]

https://bugsigdb.org/Study_845/Experiment_1/Signature_2 Ruminococcaceae [G-1] bacterium should be changed to uncultured bacteria according to the this article https://www.cytena.com/wp-content/uploads/2022/07/B.SIGHT-Sequencing-Single-cell-Genomes-of-uncultivated-bacteria-in-the-human-oral-microbiome.pdf (omojokun)

GCA-900066225[edit]

https://bugsigdb.org/Study_844/Experiment_3/Signature_1

GCA-900066225.jpg

- I discovered GCA-900066225, as GenBank assembly accession in Genome Taxonomy Database (GTDB) for Massiliimalia. I then linked it back to NCBI,Taxonomy ID: 2895461. --Joan Chuks (talk) 16:25, 18 March 2024 (UTC)

https://bugsigdb.org/Study_999/Experiment_1/Signature_2 GCA-900066225 changed to Massiliimalia (Taxonomy ID: 2895461)--Joan Chuks (talk) 18:20, 15 April 2024 (UTC)

GCA_900066575[edit]

GCA-900066575

I discovered GCA-900066575, as GenBank assembly accession in Genome Taxonomy Database (GTDB) for uncultured Clostridium sp. and I then linked back to NCBI,Taxonomy ID:59620.--Joan Chuks (talk) 16:14, 17 April 2024 (UTC)

Resolution attempt of Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort[edit]

Experiment_1/Signature_1[edit]

Signature 1-2 missing NCBI ID.png

For Prevotella_7: the taxonomic hierarchy(Kingdom to Genus) provided in the study's supplement table was the same with that of Prevotella in NCBI website, except the phylum level. The study recorded the phylum as Bacteroidetes while NCBI recorded the phylum for Prevotella as Bacteroidota. From further research (the-scientist.com), I found out that Bacteroidota is the new name for the phylum of bacteria that was previously known as Bacteroidetes. So, I updated it as Prevotella with the NCBI ID (838).

This was similar for Escherichia/Shigella, as the research showed that Pseudomonadota (Phylum name for Escherichia/Shigella sp. in NCBI) is the new name for the phylum of bacteria that was previously known as Proteobacteria (Phylum name in the study table). So, I updated it as Escherichia/Shigella sp with the NCBI ID (1940338).

Erysipelotrichaceae_unclassified seemed more like a case of a reverse of naming convention, as it appears as unclassified Erysipelotrichaceae in NCBI (ID - 544447), and was updated accordingly.

--Joan Chuks (talk) 17:46, 24 October 2023 (UTC)

Experiment_1/Signature_2[edit]

Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort/Experiment 1/Signature 2 Mollicutes_RF39_Unclassified was updated to unclassified Mollicutes which is the closest name to the family name recorded in the study's supplementary table S2c --Joan Chuks (talk) 15:38, 2 November 2023 (UTC)

Experiment_2/Signature_1 (Clostridia cluster)[edit]

Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort/Experiment 2/Signature 1


Experiment_2/Signature_2[edit]

Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort/Experiment 2/Signature 2 Mollicutes_RF39_Unclassified was updated to unclassified Mollicutes which is the closest name to the family name recorded in the study's supplementary table S2d

Some signatures are still unresolved - Ruminococcaceae_UCG-013, Lachnospiraceae_UCG-010, Erysipelotrichaceae_UCG-003, GCA-900066575, Ruminococcaceae_UCG-005 3068309 --Joan Chuks (talk) 16:03, 2 November 2023 (UTC)

Ruminococcaceae_UCG-005 & Ruminococcaceae_UCG-013 now updated to Ruminococcaceae bacterium UCG-005 (NCBI ID: 3068309

I discovered GCA-90006657 in Genome Taxonomy Database (GTDB) and then linked back to NCBI ID - 59620 which corresponds with the study's taxa hierarchy for the signature.

--Joan Chuks (talk) 01:13, 7 November 2023 (UTC)

Clostridium sensu stricto 1 has been solved as Clostridium genus with NCBI ID OF 1485. Refer to [7] [8] (Idiaru Angela)

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