Abstract
Clostridium indolis DSM 755T 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 755T 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.
Highlights
The C. saccharolyticum species group is a poorly described and taxonomically confusing clade in the Lachnospiraceae, a family within the Clostridiales that includes members of clostridial cluster XIVa [1]
Neither lactate nor citrate are utilized, other studies demonstrate that fecal isolates closely related to C. indolis may utilize lactate [29], and that the type strain DSM 755T utilizes citrate [30]
The genomes of C. indolis and its near relatives (C. saccharolyticum, C. hathewayi, and C. phytofermentans) have similar numbers of genes in each of the 25 broad COG categories, differences exist in the type and distribution of genes in specific functional groups (Table 5), those related to COG categories (G) Carbohydrate transport and metabolism, (C) Energy production and conversion, and (Q) Secondary metabolites biosynthesis, transport and catabolism
Summary
C. indolis is not well characterized, and there are conflicting reports about its physiology It is described as a sulfate reducer with the ability to ferment some simple sugars, pectin, pectate, mannitol, and galacturonate, and convert pyruvate to acetate, formate, ethanol, and butyrate [28]. According to this source, neither lactate nor citrate are utilized, other studies demonstrate that fecal isolates closely related to C. indolis may utilize lactate [29], and that the type strain DSM 755T utilizes citrate [30].
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