Growth signatures in bacterial sequence data

2015 ◽  
Vol 12 (11) ◽  
pp. 1009-1009
Keyword(s):  
Sequence Data ◽  
Bacterial Sequence

scholarly journals Intestinal transkingdom analysis on the impact of antibiotic perturbation in health and critical illness

2020 ◽  
Author(s):  
Bastiaan W. Haak ◽  
Ricard Argelaguet ◽  
Cormac M. Kinsella ◽  
Robert F.J. Kullberg ◽  
Jacqueline M. Lankelma ◽  
...  
Keyword(s):  
Critical Illness ◽  
Sequence Data ◽  
Critical Role ◽  
Invasive Disease ◽  
Intestinal Environment ◽  
Bacterial Microbiota ◽  
And Shifts ◽  
The Impact ◽  
Computational Strategy ◽  
Bacterial Sequence

AbstractBacterial microbiota play a critical role in mediating local and systemic immunity, and shifts in these microbial communities have been linked to impaired outcomes in critical illness. Emerging data indicate that other intestinal organisms, including bacteriophages, viruses of eukaryotes, fungi, and protozoa, are closely interlinked with the bacterial microbiota and their host, yet their collective role during antibiotic perturbation and critical illness remains to be elucidated. Here, multi-omics factor analysis (MOFA), a novel computational strategy to systematically integrate viral, fungal and bacterial sequence data, we describe the functional impact of exposure to broad-spectrum antibiotics in healthy volunteers and critically ill patients. We observe that a loss of the anaerobic intestinal environment is directly correlated with an overgrowth of aerobic pathobionts and their corresponding bacteriophages, as well as an absolute enrichment of opportunistic yeasts capable of causing invasive disease. These findings further illustrate the complexity of transkingdom interactions within the intestinal environment, and show that modulation of the bacterial component of the microbiome has implications extending beyond this kingdom alone.

scholarly journals Inferring Social Network Structure from Bacterial Sequence Data

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e22685 ◽  
Author(s):  
Mateusz M. Pluciński ◽  
Richard Starfield ◽  
Rodrigo P. P. Almeida
Keyword(s):  
Social Network ◽  
Network Structure ◽  
Sequence Data ◽  
Social Network Structure ◽  
Bacterial Sequence

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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