title: The complete genome sequence of Clostridium indolis DSM 755(T.).
abstract: Clostridium indolis DSM 755(T) is a bacterium commonly found in soils and the feces of birds and mammals. Despite its prevalence, little is known about the ecology or physiology of this species. However, close relatives, C. saccharolyticum and C. hathewayi, have demonstrated interesting metabolic potentials related to plant degradation and human health. The genome of C. indolis DSM 755(T) reveals an abundance of genes in functional groups associated with the transport and utilization of carbohydrates, as well as citrate, lactate, and aromatics. Ecologically relevant gene clusters related to nitrogen fixation and a unique type of bacterial microcompartment, the CoAT BMC, are also detected. Our genome analysis suggests hypotheses to be tested in future culture based work to better understand the physiology of this poorly described species.
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, MA, USA ;
authors.forename: Amy S
authors.initials: AS
authors.lastname: Biddle
authors.forename: Susan
authors.initials: S
authors.lastname: Leschine
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: James
authors.initials: J
authors.lastname: Han
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Amy
authors.initials: A
authors.lastname: Chen
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Markowitz
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Krishna
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Mikhailova
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Galina
authors.initials: G
authors.lastname: Ovchinnikova
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Schaumberg
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Stamatis
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tatiparthi
authors.initials: T
authors.lastname: Reddy
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Lobos
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Henrik P
authors.initials: HP
authors.lastname: Nordberg
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Michael N
authors.initials: MN
authors.lastname: Cantor
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Susan X
authors.initials: SX
authors.lastname: Hua
authors.affiliation: Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: ; Department of Biology, University of Massachusetts, Amherst, MA, USA ; Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA .
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Blanchard
keywords: Clostridium indolis; aromatic degradation; bacterial microcompartments; citrate; lactate; nitrogen fixation