scholarly journals The electronic tree of life (eTOL): a net of long probes to characterize the human microbiome from RNA-seq data

2021 ◽  
Author(s):  
Xinyue Hu ◽  
Jürgen Haas ◽  
Richard Lathe
Keyword(s):  
Human Tissue ◽  
Human Microbiome ◽  
Small Subunit ◽  
Tree Of Life ◽  
Alternative Methods ◽  
Target Tissue ◽  
Rna Seq ◽  
Small Subunit Rrna ◽  
Microbiome Analysis ◽  
Rrna Sequences

Abstract Background Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life. Results We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer small subunit rRNA sequences across the Tree of Life (the 'electronic tree of life', eTOL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by reconfirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. In addition, contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method, we report the use of the eTOL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved. Conclusions This generic methodology may find wider application in microbiome analysis including diagnostics.

Phylogeny of Trichomonads Inferred from Small-Subunit rRNA Sequences

1995 ◽  
Vol 42 (4) ◽  
pp. 411-415 ◽  
Author(s):  
JOHN GUNDERSON ◽  
GREGORY HINKLE ◽  
DETLEF LEIPE ◽  
HILARY G. MORRISON ◽  
SHAWN K. STICKEL ◽  
...  
Keyword(s):  
Small Subunit ◽  
Small Subunit Rrna ◽  
Rrna Sequences

scholarly journals Abundant and Diverse Fungal Microbiota in the Murine Intestine

2006 ◽  
Vol 72 (1) ◽  
pp. 793-801 ◽  
Author(s):  
Alexandra J Scupham ◽  
Laura L. Presley ◽  
Bo Wei ◽  
Elizabeth Bent ◽  
Natasha Griffith ◽  
...  
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Culture Independent ◽  
Specific Pathogen ◽  
Health And Disease ◽  
Oligonucleotide Fingerprinting ◽  
Rrna Sequences

ABSTRACT Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.

Phylogenetic Relationships among Karyorelictids and Heterotrichs Inferred from Small Subunit rRNA Sequences: Resolution at the Base of the Ciliate Tree

1995 ◽  
Vol 4 (1) ◽  
pp. 77-87 ◽  
Author(s):  
Robert P. Hirt ◽  
Patricia L. Dyal ◽  
Mark Wilkinson ◽  
Bland J. Finlay ◽  
David McL. Roberts ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Rrna Sequences

scholarly journals Novel Eukaryotic Lineages Inferred from Small-Subunit rRNA Analyses of Oxygen-Depleted Marine Environments

2003 ◽  
Vol 69 (5) ◽  
pp. 2657-2663 ◽  
Author(s):  
Thorsten Stoeck ◽  
Slava Epstein
Keyword(s):  
Salt Marsh ◽  
Phylogenetic Tree ◽  
Sequence Similarity ◽  
Small Subunit ◽  
Cape Cod ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Related Sequence ◽  
Diverse Communities ◽  
Rrna Sequences

ABSTRACT Microeukaryotes in oxygen-depleted environments are among the most diverse, as well as the least studied, organisms. We conducted a cultivation-independent, small-subunit (SSU) rRNA-based survey of microeukaryotes in suboxic waters and anoxic sediments in the great Sippewisset salt marsh, Cape Cod, Mass. We generated two clone libraries and analyzed approximately 300 clones, which contained a large diversity of microeukaryotic SSU rRNA signatures. Only a few of these signatures were closely related (sequence similarity of >97%) to the sequences reported earlier. The bulk of our sequences represented deep novel branches within green algae, fungi, cercozoa, stramenopiles, alveolates, euglenozoa and unclassified flagellates. In addition, a significant number of detected rRNA sequences exhibited no affiliation to known organisms and sequences and thus represent novel lineages of the highest taxonomical order, most of them branching off the base of the global phylogenetic tree. This suggests that oxygen-depleted environments harbor diverse communities of novel organisms, which may provide an interesting window into the early evolution of eukaryotes.

Description of Tetrahymena empidokyrea n.sp., a new species in the Tetrahymena pyriformis sibling species complex (Ciliophora, Oligohymenophorea), and an assessment of its phylogenetic position using small-subunit rRNA sequences

1996 ◽  
Vol 74 (10) ◽  
pp. 1898-1906 ◽  
Author(s):  
Cheryl A. Jerome ◽  
Denis H. Lynn ◽  
Ellen M. Simon
Keyword(s):  
New Species ◽  
Sibling Species ◽  
Species Complex ◽  
Tetrahymena Pyriformis ◽  
Small Subunit ◽  
Biological Species ◽  
Phylogenetic Position ◽  
Small Subunit Rrna ◽  
A New Species ◽  
Rrna Sequences

Ciliates infected 0.25% of adult Aedes sp. mosquitoes collected in Guelph, Ontario. Morphological observations of live and stained specimens indicated that these ciliates belonged to the Tetrahymena pyriformis sibling species complex. This study provides the first well-documented case of insects being infected by a species in the T. pyriformis complex. Mating experiments demonstrated that these "mosquito" ciliates were reproductively isolated from previously described biological species in the complex, and are designated a new species, Tetrahymena empidokyrea n.sp. Phylogenetic analysis using SSrDNA sequences suggested that T. empidokyrea n.sp. is either basal to all species in the genus Tetrahymena or basal to one of the two main lineages in that genus.

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