Case 20: Autoimmune Encephalitis with Unusual Antibodies

Arbizu, Javier; Rosales, Juan J.

doi:10.1007/978-3-030-83598-9_20

Cited by 1 publication

(1 citation statement)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Kruskal‐Wallis rank sum test for the differences in alpha diversity among more than two different sampling stations and habitat types, their pairwise comparisons using the Wilcoxon rank sum test with p ‐values adjusted by the Bonferroni method, and PERMANOVA for the differences in beta diversity among more than two sampling stations or types were performed using the R package “vegan” (Dixon, 2003 ). When beta diversity of two sampling stations or habitant types were compared, pairwise PERMANOVA test with p ‐values adjusted by the Holm method was performed using “pairwiseAdonis” package ( https://github.com/pmartinezarbizu/pairwiseAdonis ) (Arbizu, 2021 ). Significant differences between different habitats (nodule, nodule‐surface muds, sediment, bottom water and water column) in terms of relative ASV abundance were determined by linear discriminant analysis (LDA) effect size (LefSe, Segata et al, 2011 ) with default cut‐off parameters (LDA >2.0, p < 0.05).…”

Section: Methodsmentioning

confidence: 99%

Population‐level prokaryotic community structures associated with ferromanganese nodules in the Clarion‐Clipperton Zone (Pacific Ocean) revealed by 16S rRNA gene amplicon sequencing

Tominaga,

Takebe,

Murakami

et al. 2023

Environ Microbiol Rep

View full text Add to dashboard Cite

Although deep‐sea ferromanganese nodules are a potential resource for exploitation, their formation mechanisms remain unclear. Several nodule‐associated prokaryotic species have been identified by amplicon sequencing of 16S rRNA genes and are assumed to contribute to nodule formation. However, the recent development of amplicon sequence variant (ASV)‐level monitoring revealed that closely related prokaryotic populations within an operational taxonomic unit often exhibit distinct ecological properties. Thus, conventional species‐level monitoring might have overlooked nodule‐specific populations when distinct populations of the same species were present in surrounding environments. Herein, we examined the prokaryotic community diversity of nodules and surrounding environments at the Clarion‐Clipperton Zone in Japanese licensed areas by 16S rRNA gene amplicon sequencing with ASV‐level resolution for three cruises from 2017 to 2019. Prokaryotic community composition and diversity were distinct by habitat type: nodule, nodule‐surface mud, sediment, bottom water and water column. Most ASVs (~80%) were habitat‐specific. We identified 178 nodule‐associated ASVs and 41 ASVs associated with nodule‐surface mud via linear discriminant effect size analysis. Moreover, several ASVs, such as members of SAR324 and Woeseia, were highly specific to nodules. These nodule‐specific ASVs are promising targets for future investigation of the nodule formation process.

show abstract

Section: Methodsmentioning

confidence: 99%