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PMID: 22434425 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).

Genome research ·Vol. 22 ·No. 6 ·2012-06-00 ·Pages 1107-19

Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC

Abstract

Segmented filamentous bacteria (SFB) are host-specific intestinal symbionts that comprise a distinct clade within the Clostridiaceae, designated Candidatus Arthromitus. SFB display a unique life cycle within the host, involving differentiation into multiple cell types. The latter include filaments that attach intimately to intestinal epithelial cells, and from which "holdfasts" and spores develop. SFB induce a multifaceted immune response, leading to host protection from intestinal pathogens. Cultivation resistance has hindered characterization of these enigmatic bacteria. In the present study, we isolated five SFB filaments from a mouse using a microfluidic device equipped with laser tweezers, generated genome sequences from each, and compared these sequences with each other, as well as to recently published SFB genome sequences. Based on the resulting analyses, SFB appear to be dependent on the host for a variety of essential nutrients. SFB have a relatively high abundance of predicted proteins devoted to cell cycle control and to envelope biogenesis, and have a group of SFB-specific autolysins and a dynamin-like protein. Among the five filament genomes, an average of 8.6% of predicted proteins were novel, including a family of secreted SFB-specific proteins. Four ADP-ribosyltransferase (ADPRT) sequence types, and a myosin-cross-reactive antigen (MCRA) protein were discovered; we hypothesize that they are involved in modulation of host responses. The presence of polymorphisms among mouse SFB genomes suggests the evolution of distinct SFB lineages. Overall, our results reveal several aspects of SFB adaptation to the mammalian intestinal tract.

MeSH Terms
ADP Ribose Transferases/genetics,metabolism Adaptation, Physiological Amino Acid Sequence Animals Bacterial Proteins/genetics,metabolism Cell Differentiation/genetics DNA, Ribosomal Epithelial Cells/microbiology Genome, Bacterial Gram-Positive Endospore-Forming Bacteria/genetics,physiology Intestines/microbiology Mice Microfluidic Analytical Techniques Molecular Sequence Data Phylogeny Polymorphism, Genetic Sequence Analysis, DNA Single-Cell Analysis/methods
Chemicals
Bacterial Proteins DNA, Ribosomal ADP Ribose Transferases
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Pamp Sünje J
Department of Microbiology and Immunology, The Howard Hughes Medical Institute.
Harrington Eoghan D
Quake Stephen R
Relman David A
Blainey Paul C
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.131482.111
Published
2012-06-00
Epub
2012-00-20
Pages
1107-19
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC3371716
Subset
IM
Grants
NIH HHS · DP1 OD000964 · United States
NHGRI NIH HHS · R01 HG004863 · United States
NIH HHS · DP1OD000964 · United States
External Links
PubMed source DOI: 10.1101/gr.131482.111 PMC Full Text View journal details
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