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

Taxa resolution Attempts for https://bugsigdb.org/Study_911

unclassified [Eubacterium]coprostanoligenes group changed to Eubacterium coprostanoligenes (Taxonomy ID: 290054) --Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

unclassified Izemoplasmatales changed to unclassified Candidatus Izemoplasmatales (3106452), which is its Equivalent--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

Lachnospiraceae NK3A20 group changed to Lachnospiraceae bacterium NK3A20 (877406) --Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

unclassified [Clostridium] methylpentosum group - [Clostridium] methylpentosum) (84026)--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

Unclassified Erysipelatoclostridiaceae changed to unclassified Thomasclavelia (3025756)(equivalent - unclassified Erysipelatoclostridium)--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

Unclassified Ruminococcaceae changed to unclassified Oscillospiraceae (473772)--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

[Eubacterium] siraeum group changed to [Eubacterium] siraeum 1 (39492)--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

[Eubacterium] xylanophilum group changed to Eubacterium xylanophilum(39497)--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

Unclassified Bacilli RF39 changed to unclassified Bacilli (1526609)--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

Lachnospiraceae NC2004 group changed to Lachnospiraceae bacterium NC2004 (1410626)--Joan Chuks (talk) 15:26, 26 March 2024 (UTC)

[Ruminococcus gauvreauii] group resolved to Ruminococcus gauvreauii --Joan Chuks (talk) 15:53, 26 March 2024 (UTC)

Unclassified Acetivibrio sp. changed to unclassified Acetivibrio(NCBI txid -2641281)--Joan Chuks (talk) 16:09, 26 March 2024 (UTC)

Anaerostignum (a possible typo error) was changed to Anaerotignum (Taxonomy ID: 2039240); Erysipelotrichaceae UCG-006 and Erysipelotrichaceae UCG-003 updated to uncultured Erysipelotrichaceae bacterium (taxID, 331630); Prevotella 9 updated to Prevotella(NCBI TXID- 838); Unclassified Bacteroidales RF16 group was changed to unclassified Bacteroidales (Taxonomy ID: 185291) --Joan Chuks (talk) 06:29, 27 March 2024 (UTC)

Lachnospiraceae UCG-010, Lachnospiraceae UCG-001, Lachnospiraceae UCG-008, were updated to uncultured Lachnospiraceae bacterium(Taxonomy ID: 297314), Prevotellaceae UCG-001 was updated to uncultured Prevotella sp.(NCBI TXID: 159272)--Joan Chuks (talk) 06:15, 28 March 2024 (UTC)

UNRESOLVED TAXA

Unclassified UCG-009, Unclassified UCG-003, Unclassified UCG-004, Unclassified UCG-008, Unclassified UCG-010, Unclassified UCG-005, unclassified UCG-002, unclassified RF39,--Joan Chuks (talk) 08:18, 27 March 2024 (UTC)

unclassified Clostridiales bacterium, Unclassified Clostridia UCG-014, Unclassified Clostridia vadinBB60 group, Unclassified vadinBE97, unclassified Kiritimatiellae WCHB-1-41, unclassified WCHB-1-41,--Joan Chuks (talk) 08:18, 27 March 2024 (UTC)

Lachnospiraceae FCS020 group, Lachnospiraceae ND3007 group,--Joan Chuks (talk) 08:18, 27 March 2024 (UTC)

Prevotellaceae NK3B31 group,-Joan Chuks (talk) 08:18, 27 March 2024 (UTC)

Rikenellaceae RC9 gut group, Family XIII AD3011 group,--Joan Chuks (talk) 08:18, 27 March 2024 (UTC)

EMP-G18, Z20, CAG-352, dgA-11 gut group, Incertae Sedis, NK4A214--Joan Chuks (talk) 08:18, 27 March 2024 (UTC)

Author's feedback

Thank you for putting this together, it is such an effort to standardize this info for others, kudos to the team that did a great job!

I've found some minor info you may want to update:

-Perhaps it is a constraint you have in the way of coding data into the portal but the ANCOM-BC approach was performed with AGE as covariate, not categorical variable (like the Alpha diversity analyses), the plot Fig 4A shows the +-1SD against the mean just to visualize results.

-For the alpha diversity analyses we ran GLMMs with a full-null model comparison on several metrics: pure richness-based estimators (ObservedASVs, ACE; Model 1a-1b), Faith’s phylogenetic diversity (PD) as phylogenetic richness estimator (Model 1c), and richness-evenness estimators (i.e., Shannon-Weaver, Inverse Simpson: Model 1d-1e).

-Concerning the experiment 12, the group names MOT, MST, SST are just group names for my team, they are not related to any maternal or social characteristic of the subject, it could be group A, B and C...perhaps you could write just the group name? It's up to you. Other than that, thank you so much to the team for investing in this, I am sure it was a hard job.

Cheers, Simo_