Saturday, February 16, 2013

Waiting For The Human Intestinal Eukaryotome

We were lucky enough to have a paper accepted for publication in the ISME Journal (Nature Publishing Group) in which we call for data on the "human intestinal eukaryotome".

In the paper, we start out:

"Recent developments in Next Generation Sequencing (NGS) technologies have allowed culture-independent and deep molecular analysis of the microbial diversity in faecal samples, and have provided new insights into the bacterial composition of the distal gut microbiota. Studies of the microbiome in different patient groups using metagenomics or 16S rRNA gene sequencing are increasing our knowledge of how the microbiota influences health and disease. The majority of recent advances in our understanding of human microbiota structure and dynamic changes in disease were made through phylogenetic interrogation of small subunit (SSU) rRNA (Paliy and Agans 2012). However, until recently such studies have generally failed to include data on common eukaryotic, endobiotic organisms such as single-celled parasites and yeasts ('micro-eukaryotes'). This deficiency may strongly bias the interpretation of results and ignoring an entire kingdom of organisms is a major limitation of human microbiome studies."

We address shortcomings of state-of-the-art methodologies used to explore micro-eukaryotic communities and suggest directions for future research.

The full paper is accessed here (to read this article in full you may need to log in, make a payment or gain access through a site license).

Along these lines, there has a publication out just now in PLoS One on "Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities, which can be accessed for free here.

For other interesting papers on a similar topic, see "suggested reading" below.

Suggested reading:
Andersen LO, Vedel Nielsen H, & Stensvold CR (2013). Waiting for the human intestinal Eukaryotome. The ISME journal PMID: 23407309

Kittelmann, S., Seedorf, H., Walters, W., Clemente, J., Knight, R., Gordon, J., & Janssen, P. (2013). Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities PLoS ONE, 8 (2) DOI: 10.1371/journal.pone.0047879

Scanlan PD, & Marchesi JR (2008). Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. The ISME journal, 2 (12), 1183-93 PMID: 18670396

Pandey PK, Siddharth J, Verma P, Bavdekar A, Patole MS, & Shouche YS (2012). Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers. Journal of biosciences, 37 (2), 221-6 PMID: 22581327
Hamad, I., Sokhna, C., Raoult, D., & Bittar, F. (2012). Molecular Detection of Eukaryotes in a Single Human Stool Sample from Senegal PLoS ONE, 7 (7) DOI: 10.1371/journal.pone.0040888
Paliy O, & Agans R (2012). Application of phylogenetic microarrays to interrogation of human microbiota. FEMS microbiology ecology, 79 (1), 2-11 PMID: 22092522

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