Open Access

The complete genome sequence of Clostridium indolis DSM 755T

  • Amy S. Biddle1, 2Email author,
  • Susan Leschine3,
  • Marcel Huntemann4,
  • James Han4,
  • Amy Chen4,
  • Nikos Kyrpides4,
  • Victor Markowitz4,
  • Krishna Palaniappan4,
  • Natalia Ivanova4,
  • Natalia Mikhailova4,
  • Galina Ovchinnikova4,
  • Andrew Schaumberg4,
  • Amrita Pati4,
  • Dimitrios Stamatis4,
  • Tatiparthi Reddy4,
  • Elizabeth Lobos4,
  • Lynne Goodwin4,
  • Henrik P. Nordberg4,
  • Michael N. Cantor4,
  • Susan X. Hua4,
  • Tanja Woyke4 and
  • Jeffrey L. Blanchard2, 5, 6
Standards in Genomic Sciences20149:9031089

DOI: 10.4056/sigs.5281010

Published: 15 June 2014

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.

Keywords

Clostridium indolis citrate lactate aromatic degradation nitrogen fixation bacterial microcompartments

Introduction

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]. This group includes C. indolis, C. sphenoides, C. methoxybenzovorans, C. celerecrescens, and Desulfotomaculum guttoideum, none of which are well studied (Figure 1). C. saccharolyticum has gained attention because its saccharolytic capacity was shown to be syntrophic with the cellulolytic activity of Bacteroides cellulosolvens in co-culture, enabling the conversion of cellulose to ethanol in a single step [6,7]. Members of this group, such as C. celerecrescens, are themselves cellulolytic [8], and others are known to degrade unusual substrates such as methylated aromatic compounds (C. methoxybenzovorans) [9], and the insecticide lindane (C. sphenoides) [10]. C. indolis was targeted for whole genome sequencing to provide insight into the genetic potential of this taxa that could then direct experimental efforts to understand its physiology and ecology.
Figure 1.

Phylogenetic tree based on 16S rRNA gene sequences highlighting the position of Clostridium indolis relative to other type strains (T) within the Lachnospiraceae. The strains and their corresponding NCBI accession numbers (and, when applicable, draft sequence coordinates) for 16S rRNA genes are: Desulfotomaculum guttoideum strain DSM 4024T, Y11568; C. sphenoides ATCC 19403T, AB075772; C. celerecrescens DSM 5628T, X71848; C. indolis DSM 755T, Pending release by JGI: 1620643–1622056; C. methoxybenzovorans SR3, AF067965; C. saccharolyticum WM1T, NC_014376:18567-20085; C. algidixylanolyticum SPL73T, AF092549; C. hathewayi DSM 13479T, ADLN00000000: 202–1639; Eubacterium eligens L34420 T, L34420; Ruminococcus gnavus ATCC 29149T, X94967; R. torques ATCC 27756T, L76604; E. rectale L34627T; Roseburia intestinalis L1-82T, AJ312385; R. hominis A2-183T, AJ270482; C. jejuense HY-35-12T, AY494606; C. xylanovorans HESP1T, AF116920; C. phytofermentans ISDgT, CP000885: 15754–17276. The tree uses sequences aligned by MUSCLE, and was inferred using the Neighbor-Joining method [2]. The optimal tree with the sum of branch lengths = 0.50791241 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches [3]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method [4] and are in the units of the number of base substitutions per site. Evolutionary analyses were conducted in MEGA 5 [5]. C. stercorarium ATCC 35414T, CP003992: 856992–858513 was used as an outgroup.

Classification and features

The general features of Clostridium indolis DSM 755T are listed in Table 1. C. indolis DSM 755T was originally named for its ability to hydrolyze tryptophan to indole, pyruvate, and ammonia [23] in the classic Indole Test used to distinguish bacterial species. It has been isolated from soil [24], feces [25], and clinical samples from infections [27]. Despite its prevalence, 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, however 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]. It is unclear whether C. indolis is able to make use of a wider range of sugars or break down complex carbohydrates, however growth is reported to be stimulated by fermentable carbohydrates [28].
Table 1.

Classification and general features of Clostridium indolis DSM 755T

MIGS ID

Property

Term

Evidence Code

 

Current classification

Domain Bacteria

TAS [11]

 

Phylum Firmicutes

TAS [1214]

 

Class Clostridia

TAS [15,16]

 

Order Clostridiales

TAS [17,18]

 

Family Lachnospiraceae

TAS [15,19]

 

Genus Clostridium

TAS [17,20,21]

 

Species Clostridium indolis

TAS [17,22]

 

Type strain DSM 755

 
 

Gram stain

Negative

TAS [23,24]

 

Cell shape

Rod

TAS [23,24]

 

Motility

Motile

TAS [23,24]

 

Sporulation

Terminal, spherical spores

TAS [23,24]

 

Temperature range

Mesophilic

TAS [23,24]

 

Optimum temperature

37°C

TAS [23,24]

 

Carbon sources

Glucose, lactose, sucrose, mannitol, pectin, pyruvate, others

TAS [23,24]

 

Terminal electron receptor

Sulfate

TAS [23,24]

 

Indole test

Positive

TAS [23,24]

MIGS-6

Habitat

Isolated from soil, feces, wounds

TAS [24,25]

MIGS-6.3

Salinity

Inhibited by 6.5% NaCl

TAS [23,24]

MIGS-22

Oxygen

Anaerobic

TAS [23,24]

MIGS-15

Biotic relationship

Free living and host associated TAS [24,25],9

 

MIGS-14

Pathogenicity

No NAS

 

MIGS-4

Geographic location

Soil, feces TAS [24,25],9

 

Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [26].

Genome sequencing information

Genome project history

The genome was selected based on the relatedness of C. indolis DSM 755T to C. saccharolyticum, an organism with interesting saccharolytic and syntrophic properties. The genome sequence was completed on May 2, 2013, and presented for public access on June 3, 2013. Quality assurance and annotation done by DOE Joint Genome Institute (JGI) as described below. Table 2 presents a summary of the project information and its association with MIGS version 2.0 compliance [31].
Table 2.

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Improved Draft

MIGS-28

Libraries used

Shotgun and long insert mate pair (Illumina), SMRTbellTM (PacBio)

MIGS-29

Sequencing platforms

Illumina and PacBio

MIGS-31.2

Fold coverage

759.7× (Illumina), 51.6× (PacBio)

MIGS-30

Assemblers

Velvet, AllpathsLG

MIGS-32

Gene calling method

Prodigal, GenePRIMP

 

Genome Database release

June 3, 2013 (IMB)

 

Genbank ID

Pending release by JGI

 

Genbank Date of Release

Pending release by JGI

 

GOLD ID

Gi22434

 

Project relevance

Anaerobic plant degradation

Growth conditions and DNA isolation

C. indolis DSM 755T was cultivated anaerobically on GS2 medium as described elsewhere [32]. DNA for sequencing was extracted using the DNA Isolation Bacterial Protocol available through the JGI (http://www.jgi.doe.gov). The quality of DNA extracted was assessed by gel electrophoresis and NanoDrop (ThermoScientific, Wilmington, DE) according to the JGI recommendations, and the quantity was measured using the Quant-iTTM Picogreen assay kit (Invitrogen, Carlsbad, CA) as directed.

Genome sequencing and assembly

The draft genome of C. indolis was generated at the DOE Joint genome Institute (JGI) using a hybrid of the Illumina and Pacific Biosciences (PacBio) technologies. An Illumina std shotgun library and long insert mate pair library was constructed and sequenced using the Illumina HiSeq 2000 platform [33]. 16,165,490 reads totaling 2,424.8 Mb were generated from the std shotgun and 26,787,478 reads totaling 2,437.7 Mb were generated from the long insert mate pair library. A Pacbio SMRTbellTM library was constructed and sequenced on the PacBio RS platform. 99,448 raw PacBio reads yielded 118,743 adapter trimmed and quality filtered subreads totaling 330.2 Mb. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts [34]. Filtered Illumina and PacBio reads were assembled using AllpathsLG (PrepareAllpathsInputs: PHRED 64=1 PLOIDY=1 FRAG COVERAGE=50 JUMP COVERAGE=25; RunAllpath-sLG: THREADS=8 RUN=std pairs TARGETS=standard VAPI WARN ONLY=True OVERWRITE=True) [35]. The final draft assembly contained 1 contig in 1 scaffold. The total size of the genome is 6.4 Mb. The final assembly is based on 2,424.6 Mb of Illumina Std PE, 2,437.6 Mb of Illumina CLIP PE and 330.2 Mb of PacBio post filtered data, which provides an average 759.7× Illumina coverage and 51.6× PacBio coverage of the genome, respectively.

Genome annotation

Genes were identified using Prodigal [36], followed by a round of manual curation using GenePRIMP [9] for finished genomes and Draft genomes in fewer than 10 scaffolds. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool [37] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [38]. Other non-coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL [39]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG) platform [40] developed by the Joint Genome Institute, Walnut Creek, CA, USA [41]. Information in the tables below reflects the gene information in the JGI annotation on the IMG website [40].

Genome properties

The genome of C. indolis DSM 755 consists of a 6,383,701 bp circular chromosome with GC content of 44.93% (Table 3). Of the 5,903 genes predicted, 5,802 were protein-coding genes, and 101 RNAs; 170 pseudogenes were also identified. 81.21% of genes were assigned with a putative function with the remaining annotated as hypothetical proteins. The genome summary and distribution of genes into COGs functional categories are listed in Tables 3 and 4.
Table 3.

Nucleotide content and gene count levels of the genome of C. indolis DSM 755

Attribute

Value

% of totala

Genome size (bp)

6,383,701

 

DNA Coding region (bp)

5,688,007

89.10

DNA G+C content (bp)

2,868,247

44.93

Total genesb

5,903

100.00

RNA genes

101

1.71

Protein-coding genes

5,802

98.29

Protein-coding with function pred.

4,794

81.21

Genes in paralog clusters

4,527

76.69

Genes assigned to COGs

4,643

78.65

Genes with signal peptides

421

7.13

Genes with transmembrane helices

1,494

25.31

Paralogous groups

4,527

76.69

a) The total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome. b) Also includes 170 pseudogenes.

Table 4.

Number of genes in C. indolis DSM 755 associated with the 25 general COG functional categories

Code

Value

%agea

Description

J

184

3.57

Translation

A

0

0

RNA processing and modification

K

531

10.30

Transcription

L

191

3.71

Replication, recombination and repair

B

1

0.02

Chromatin structure and dynamics

D

28

0.54

Cell cycle control, mitosis and meiosis

Y

0

0

Nuclear structure

V

107

2.08

Defense mechanisms

T

335

6.50

Signal transduction mechanisms

M

235

4.56

Cell wall/membrane biogenesis

N

70

1.36

Cell motility

Z

0

0

Cytoskeleton

W

0

0

Extracellular structures

U

41

0.80

Intracellular trafficking and secretion

O

124

2.41

Posttranslational modification, protein turnover, chaperones

C

261

5.06

Energy production and conversion

G

910

17.65

Carbohydrate transport and metabolism

E

493

9.56

Amino acid transport and metabolism

F

110

2.13

Nucleotide transport and metabolism

H

153

2.97

Coenzyme transport and metabolism

I

77

1.49

Lipid transport and metabolism

P

325

6.30

Inorganic ion transport and metabolism

Q

70

1.36

Secondary metabolites biosynthesis, transport and catabolism

R

590

11.45

General function prediction only

S

319

6.19

Function unknown

-

1260

21.35

Not in COGs

a) The total is based on the total number of protein coding genes in the annotated genome.

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 (not shown), however differences exist in the type and distribution of genes in specific functional groups (Table 5), particularly those related to COG categories (G) Carbohydrate transport and metabolism, (C) Energy production and conversion, and (Q) Secondary metabolites biosynthesis, transport and catabolism.

Table 5.

Number of genes in each of the 25 general COG functional categoriesa found in C. indolis DSM 755T but not in closely related species

Code

Value

Description

J

4

Translation

A

0

RNA processing and modification

K

5

Transcription

L

9

Replication, recombination and repair

B

1

Chromatin structure and dynamics

D

0

Cell cycle control, mitosis and meiosis

Y

0

Nuclear structure

V

1

Defense mechanisms

T

2

Signal transduction mechanisms

M

8

Cell wall/membrane biogenesis

N

2

Cell motility

Z

0

Cytoskeleton

W

0

Extracellular structures

U

1

Intracellular trafficking and secretion

O

10

Posttranslational modification, protein turnover, chaperones

C

28

Energy production and conversion

G

6

Carbohydrate transport and metabolism

E

8

Amino acid transport and metabolism

F

1

Nucleotide transport and metabolism

H

11

Coenzyme transport and metabolism

I

2

Lipid transport and metabolism

P

11

Inorganic ion transport and metabolism

Q

10

Secondary metabolites biosynthesis, transport and catabolism

R

18

General function prediction only

S

21

Function unknown

a) Number of genes from a set of 158 genes not found in near relatives (C. saccharolyticum, C. phytofermentans, C. hathewayi) associated with the 25 general COG functional categories.

Carbohydrate transport and metabolism

Plant biomass is a complex composite of fibrils and sheets of cellulose, hemicellulose, waxes, pectin, proteins, and lignin. Bacteria from soil and the gut generally possess a variety of genes to degrade and transport the diversity of substrates encountered in these plant-rich environments. The genome of C. indolis includes 910 genes (17.65% of total protein coding genes) in this COG group including glycoside hydrolases with the potential to degrade complex carbohydrates including starch, cellulose, and chitin (Table 6), as well as an abundance of carbohydrate transporters (Figure 2). Almost 8% of the protein-coding genes in the genome of C. indolis were found to be associated with carbohydrate transport, represented by two main strategies. ABC (ATP binding cassette) transporters tend to carry oligosaccharides, and have less affinity for hexoses [43,44], while PTS (phosphotransferase system) transporters carry many different mono- and disaccharides, especially hexoses [45]. PTS systems provide a means of regulation via catabolite repression [46], and are thought to enable bacteria living in carbohydrate-limited environments to more efficiently utilize and compete for substrates [46]. Both C. indolis and its near relatives are more highly enriched in ABC than PTS transporters (Fig 2), however nearly a third of C. indolis and C. saccharolyticum transporters are PTS genes, suggesting a preference for hexoses, as well as an adaptation to more marginal environments. C. indolis also possesses ten genes associated with all three components of the TRAP-type C4-dicarboxylate transport system, which transports C4-dicarboxylates such as formate, succinate, and malate [47], as well as six putative malate dehydrogenases and two putative succinate dehydrogenases suggesting that C. indolis may have the potential to utilize both of these short chain fatty acids.
Figure 2.

Distribution of ABC and PTS transporters in the genomes of C. indolis and related genomes determined from Integrated Microbial Genome (IMG) annotation [40] viewed based on (a) Total umber of COGS, and (b) Percentage of genes in the genome.

Table 6.

Selected carbohydrate active genes in the C. indolis DSM 755T genome

Gene count

Product namea

Database IDb

19

Beta-glucosidase (GH-1)

EC:3.2.1.86

  

EC:3.2.1.23

 

Beta-galactosidase/

EC:3.2.1.25

8

beta-glucuronidase (GH-2)

EC:3.2.1.31

 

Beta-glucosidase/related

EC:3.2.1.21

7

glucosidases (GH-3)

EC:3.2.1.52

  

EC:3.2.1.86

 

Alpha-galactosidases/

EC:3.2.1.122

14

6-phospho-beta-glucosidases (GH-4)

EC:3.2.1.22

2

Cellulase, endogluconase (GH-5)

EC:3.2.1.4

  

EC:3.2.1.10

  

EC:3.2.1.20

  

EC:2.4.1.7

14

Alpha-amylase

EC:3.2.1.70

8

Beta-xylosidase (GH 39)

EC:3.2.1.37

2

Chitinase (GH 18)

EC:3.2.1.14

a) GH designations given from the CAZy database [42]. b) Enzyme Commission (EC) numbers assigned by the Integrated Microbial Genome (IMG) database [41].

Energy production and conversion

The genome of C. indolis contains 261 genes in COG category (C) Energy production and conversion, 28 of which are not found in the near relatives analyzed, including genes for citrate utilization (Table 7) and nitrogen fixation (Table 8).
Table 7.

Selection of C. indolis DSM 755 genes related to citrate utilization.

Locus Tag

Putative Gene Producta

Gene IDa

K401DRAFT_2892

holo-ACP synthase (CitX)

EC:2.7.7.61

K401DRAFT_2893

citrate lyase acyl carrier (CitD)

EC:4.1.3.6

K401DRAFT_2894

citrate lyase beta subunit (CitE)

EC:4.1.3.6

  

EC:2.8.3.10

K401DRAFT_2895

citrate lyase alpha subunit (CitF)

EC:4.1.3.6

  

EC:2.8.3.10

K401DRAFT_2896

triphosphoribosyl-dephospho-CoA synthase (CitG)

EC:2.7.8.25

K401DRAFT_2897

citrate (pro3S)-lyase ligase (CitC)

EC:6.2.1.22

K401DRAFT_2898

response regulator, CheY-like receiver domain, winged helix DNA binding domain

-

K401DRAFT_2899

signal transduction histidine kinase

-

K401DRAFT_2900

citrate transporter, CITMHS family

KO:K03303

  

TC.LCTP

Gene products and Enzyme Commission (EC) numbers assigned by the Integrated Microbial Genome (IMG) database [41].

Table 8.

Selection of C. indolis DSM 755 genes related to nitrogen fixation.

Locus Tag

Putative Gene Product

Gene ID

K401DRAFT_0533

nitrogenase Mo-Fe protein, α and β chains

pfam00148

K401DRAFT_0534

nitrogenase Mo-Fe protein, α and β chains

pfam00148

K401DRAFT_0535

nitrogenase subunit (ATPase) (nifH)

pfam00142

K401DRAFT_0884

nitrogenase Mo-Fe protein, α and β chains

pfam00148

K401DRAFT_0885

nitrogenase Mo-Fe protein, α and β chains

pfam00148

K401DRAFT_0886

nitrogenase subunit (ATPase) (nifH)

pfam00142

K401DRAFT_3349

nitrogenase Mo-Fe protein, α and β chains

pfam00148

K401DRAFT_3350

nitrogenase Mo-Fe protein, α and β chains

pfam00148

K401DRAFT_3351

nitrogenase subunit (ATPase) (nifH)

pfam00142

K401DRAFT_3874

nitrogenase Mo-Fe protein, α and β chains (nifD)

pfam00148

K401DRAFT_3875

nitrogenase Mo-Fe protein, α and β chains (nifK)

pfam00148

K401DRAFT_3876

nitrogenase Fe protein

pfam00142

K401DRAFT_3878

nitrogenase Mo-Fe protein, α and β chains (nifD)

pfam00148

K401DRAFT_3879

nitrogenase Mo-Fe protein, α and β chains (nifK)

pfam00148

K401DRAFT_3880

dinitrogenase Fe-Mo cofactor, (nifH)

pfam02579

K401DRAFT_3895

nitrogenase Mo-Fe protein, α and β chains (nifD)

pfam00148

K401DRAFT_3896

nitrogenase Mo-Fe protein, α and β chains (nifK)

pfam00148

K401DRAFT_5519

nitrogenase Mo-Fe protein, α and β chains (nifB)

pfam04055

K401DRAFT_5520

nitrogenase Mo-Fe protein, α and β chains (nifE)

pfam00148

K401DRAFT_5521

nitrogenase Mo-Fe protein (nifK)

pfam00148

K401DRAFT_5522

nitrogenase component 1, alpha chain (nifN-like)

pfam00148

K401DRAFT_5525

nitrogenase subunit (ATPase) (nifH)

pfam00142

Nitrogenase genes have a common gene identifier (EC:1.18.6.1), therefore the pfam numbers are given to distinguish between subunits. Gene product names and pfam numbers assigned by the Integrated Microbial Genome (IMG) database [41].

Citrate utilization

Citrate is a metabolic intermediary found in all living cells. In aerobic bacteria, citrate is utilized as part of the tricarboxylic acid (TCA) cycle. In anaerobes, citrate is fermented to acetate, formate, and/or succinate. The first step is the conversion of citrate to acetate and oxaloacetate in a reaction catalyzed by citrate lyase (EC:4.1.3.6) [48]. C. sphenoides, a close relative of C. indolis that does not yet have a sequenced genome has been shown to utilize citrate [49], but there is conflicting evidence as to whether this phenotype is present in C. indolis [28,30]. The genome of C. indolis reveals a group of seven citrate genes organized in a cluster similar to operons found in other bacterial species [48,50] (Figure 3) including CitD, CitE, and CitF, the three subunits of the citrate lyase gene [48], CitG and CitX which have been shown to be necessary for citrate lyase function [50], CitMHS, a citrate transporter, and a putative two component system similar to citrate regulatory mechanisms in other bacteria [51].
Figure 3.

Citrate utilization genes are in a single gene cluster on K401DRAFT_scaffold0000.1.1, including the citrate transporter CitMHS, and a putative two-component system.

Nitrogen Fixation

Nitrogen fixation has been observed in other clostridia [52,53] but has not been demonstrated in the C. saccharolyticum species group. It has been suggested that the capacity to fix nitrogen confers a selective advantage to cellulolytic microbes that live in nitrogen limited environments such as many soils [52]. The functional summary suggests that C. indolis can fix nitrogen. The C. indolis genome reveals 22 nitrogenase related genes in four gene clusters (Table 8), none of which are found in the near relatives analyzed in this study. A minimum set of six genes encoding for structural and biosynthetic components of a functional nitrogenase complex have been hypothesized [54]. Genes needed for the nitrogenase structural component proteins (nifH, nifD, and nifK) are present in C. indolis, but one of the three genes required to synthesize the nitrogenase iron-molybdenum cofactor (nifN) is not identified. Follow up experiments are needed to determine whether C. indolis can fix nitrogen as predicted by the genome analysis.

Lactate utilization

The genome of C. indolis includes both D- and L-lactate dehydrogenases, which convert lactate to pyruvate. Additionally, there is a lactate transporter, suggesting that C. indolis is able to utilize exogenous lactate [Table 9].
Table 9.

Selection of C. indolis DSM 755 genes related to lactate utilization.

Locus Tag

Putative Gene Product

Gene ID

K401DRAFT_1877

L-lactate dehydrogenase

EC:1.1.1.27

K401DRAFT_5775

L-lactate dehydrogenase

EC:1.1.1.27

K401DRAFT_3431

L-lactate transporter, LctP family

TC.LCTP

K401DRAFT_3220

D-lactate dehydrogenase

EC:1.1.1.28

Annotations assigned by the Integrated Microbial Genome (IMG) database [41]

Bacterial microcompartments (BMC)

The C. indolis genome contains genes associated with bacterial microcompartment shell proteins. Bacterial microcompartments (BMCs) are proteinaceous organelles involved in the metabolism of ethanolamine, 1,2-propanediol, and possibly other metabolites (Rev in [5557]). BMCs are often encoded by a single operon or contiguous stretch of DNA. The different metabolic types of BMCs can be distinguished by a key enzyme (e.g., ethanolamine lyase and propanediol dehydratase) related to its metabolic function. While the other associated genes in the operon can vary, they frequently include an alcohol dehydrogenase, an aldehyde dehydrogenase, an aldolase and an oxidoreductase.

In C. indolis there are 2 separate genetic loci that code for BMCs (Table 10 and 11 and Figure 4). One C. indolis locus (Table 10) contains a gene (K401DRAFT_2189) with sequence similarity to a B12-independent propanediol dehydratase found in Roseburia inulinivorans and Clostridium phytofermentans [58,59] (both members of the Lachnospiraceae). This enzyme has been shown to be involved in the metabolism of fucose and rhamnose [58,59] and was subsequently categorized as the glycyl radical prosthetic group-based (grp) BMC [60]. The glycyl radical family of enzymes was recently expanded to include a choline trimethylamine lyase activity that is part of a microcompartment loci in Desulfovibrio desulfuricans [61]. The corresponding C. indolis enzymes (K401DRAFT_2189 and K401DRAFT_2190) are more similar to the D. desulfuricans protein, but there are differences in the gene content of the microcompartment loci. Further work is needed to determine the physiological role of this microcompartment.
Figure 4.

CoAT BMC operon found in C. indolis, Caldalkalibacillus thermarum, C. stricklandii, C. saccharolyticum, and Bacillus selenitrireducens. Gene details are found in Table 11.

Table 10.

grp-BMC genes found in the C. indolis genome.

Locus Tag

Product Name

Gene ID/Protein Information

K401DRAFT_2181

Predicted transcriptional regulator

COG0789

K401DRAFT_2182

Predicted membrane protein

COG2510

K401DRAFT_2183

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_2184

Predicted membrane protein

pfam00936

K401DRAFT_2185

Hypothetical protein

-

K401DRAFT_2186

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_2187

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_2188

NAD-dependent aldehyde dehydrogenase

pfam00171

K401DRAFT_2189

Pyruvate formate lyase

pfam02901

K401DRAFT_2190

Pyruvate formate lyase activating enzyme

pfam04055

K401DRAFT_2191

Ethanolamine utilization protein

pfam00936

K401DRAFT_2192

Ethanolamine utilization protein

pfam10662

K401DRAFT_2193

Alcohol dehydrogenase, class IV

pfam00465

K401DRAFT_2194

Ethanolamine utilization cobalamin adenosyltransferase

COG4892

K401DRAFT_2195

Ethanolamine utilization protein, possible chaperonin

COG4820

K401DRAFT_2196

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_2197

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam03319

K401DRAFT_2198

Ethanolamine utilization protein

pfam06249

K401DRAFT_2199

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_2200

NAD-dependent aldehyde dehydrogenase

pfam00171

K401DRAFT_2201

Propanediol utilization protein

pfam06130

K401DRAFT_2202

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

Annotations assigned by the Integrated Microbial Genome (IMG) database [41].

Table 11.

CoAT BMC genes found in the C. indolis genome.

Locus Tag

Product Name

Gene ID/Protein Information

K401DRAFT_4970

DeoRC transcriptional regulator

pfam00455

K401DRAFT_4969

fucA, L-fuculose-phosphate aldolase

EC:4.1.2.17

K401DRAFT_4968

pduP, propionaldehyde dehydrogenase

pfam00171

K401DRAFT_4967

eutM, ethanolamine utilization protein

pfam00936

K401DRAFT_4966

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_4965

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_4964

Carbon dioxide concentrating mechanism/carboxysome shell protein

pfam00936

K401DRAFT_4963

Pdul, propanediol utilization protein

pfam06130

K401DRAFT_4962

eutN_CcmL

pfam03319

K401DRAFT_4961

SBP_bac_8, ABC-type sugar transporter

pfam13416

K401DRAFT_4960

Uncharacterized NAD(FAD)-dependent dehydrogenase

COG0446

K401DRAFT_4959

CoA-transferase

pfam01144

K401DRAFT_4958

CoA-transferase

pfam01144

K401DRAFT_4957

Fe-ADH, Alcohol dehydrogenase

pfam00465

Annotations assigned by the Integrated Microbial Genome (IMG) database [41]

The second C. indolis BMC loci (Table 11 and Figure 4) is even more enigmatic. This loci contains the shell proteins, alcohol dehydrogenase, aldehyde dehydrogenase, aldolase and oxidoreductase commonly found in microcompartments, but it lacks a known key enzyme. Homologs of this operon were found in four other bacterial species (Figure 4). They are all missing a known key enzyme and contain 2 genes annotated as CoA-transferase. We propose that the C. indolis genome and these other bacteria contain a novel type of microcompartment, designated the CoAT BMC. It is not clear that the function of the 2 annotated CoA-transferase genes are as predicted and further research is needed to demonstrate the physiological role of this BMC.

Secondary metabolites biosynthesis, transport and catabolism

Protocatechuate and other aromatics are intermediaries in the degradation of lignin in plant rich environments [62]. The genome of C. indolis contains two protocatechuate dioxygenases and an aromatic hydrolase, revealing the potential for utilizing aromatic compounds (Table 12).
Table 12.

Selection of C. indolis DSM 755T genes related to degradation of aromatics.

Locus Tag

Putative Gene Product

Gene ID

K401DRAFT_3571

Protocatechuate 3,4-dioxygenase beta subunit

EC:1.13.11.3

K401DRAFT_3568

Protocatechuate 3,4-dioxygenase beta subunit

EC:1.13.11.3

  

EC:5.3.3.3

K401DRAFT_3412

Aromatic ring hydroxylase

EC:4.2.1.120

Annotations assigned by the Integrated Microbial Genome (IMG) database [41]

Conclusion

The genomic sequence of C. indolis reported here reveals the metabolic potential of this organism to utilize a wide assortment of fermentable carbohydrates and intermediates including citrate, lactate, malate, succinate, and aromatics, and points to potential ecological roles in nitrogen fixation and ethanolamine utilization. Further culture-based characterization is necessary to confirm the metabolic activity suggested by this genomic analysis, and to expand the description of C. indolis.

Abbreviations

DSM: 

German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany)

ATCC: 

American Type Culture Collection (Manassas, VA, USA)

Authors’ Affiliations

(1)
Department of Microbiology, University of Massachusetts
(2)
Institute for Cellular Engineering, University of Massachusetts
(3)
Department of Veterinary and Animal Sciences, University of Massachusetts
(4)
Joint Genome Institute
(5)
Department of Biology, University of Massachusetts
(6)
Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts

References

  1. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JA. The phylogeny of the genusClostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994; 44:812–826. PubMed http://dx.doi.org/10.1099/00207713-44-4-812View ArticlePubMedGoogle Scholar
  2. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425. PubMedPubMedGoogle Scholar
  3. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791. http://dx.doi.org/10.2307/2408678View ArticleGoogle Scholar
  4. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 2004; 101:11030–11035. PubMed http://dx.doi.org/10.1073/pnas.0404206101PubMed CentralView ArticlePubMedGoogle Scholar
  5. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011; 28:2731–2739. PubMed http://dx.doi.org/10.1093/molbev/msr121PubMed CentralView ArticlePubMedGoogle Scholar
  6. Murray WD, Khan AW. Clostridium saccharolyticum sp. nov., a saccharolytic species from sewage sludge. Int J Syst Bacteriol 1982; 32:132–135. http://dx.doi.org/10.1099/00207713-32-1-132View ArticleGoogle Scholar
  7. Murray WD. Symbiotic relationship ofBacteroides cellulosolvens and Clostridium saccharolyticumin cellulose fermentation. Appl Environ Microbiol 1986; 51:710–714. PubMedPubMed CentralPubMedGoogle Scholar
  8. Palop ML, Valles S, Pinaga F, Flors A. Isolation and Characterization of an Anaerobic, Cellulolytic Bacterium, Clostridium celerecrescens sp. nov. Int J Syst Bacteriol 1989; 39:68–71. http://dx.doi.org/10.1099/00207713-39-1-68View ArticleGoogle Scholar
  9. Mechichi T, Patel BKC, Sayadi S. Anaerobic degradation of methoxylated aromatic compounds by Clostridium methoxybenzovorans and a nitrate-reducing bacterium Thauera sp. strain Cin3,4. Int Biodeterior Biodegradation 2005; 56:224–230. http://dx.doi.org/10.1016/j.ibiod.2005.09.001View ArticleGoogle Scholar
  10. Heritage AD, MacRae IC. Degradation of lindane by cell-free preparations ofClostridium sphenoides. Appl Environ Microbiol 1977; 34:222–224. PubMedPubMed CentralPubMedGoogle Scholar
  11. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  12. Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1–6. http://dx.doi.org/10.1099/00207713-28-1-1View ArticleGoogle Scholar
  13. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119–169.View ArticleGoogle Scholar
  14. Murray RGE. The Higher Taxa, or, a Place for Everything…? In: Holt JG (ed), Bergey’s Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31–34.Google Scholar
  15. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469–472. http://dx.doi.org/10.1099/ijs.0.022855-0
  16. Rainey FA. Class II. Clostridia class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.Google Scholar
  17. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225View ArticleGoogle Scholar
  18. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1–692.Google Scholar
  19. Rainey FA. Family V. Lachnospiraceae fam. nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 921.Google Scholar
  20. Prazmowski A. “Untersuchung über die Entwickelungsgeschichte und Fermentwirking einiger Bakterien-Arten.” Ph.D. Dissertation, University of Leipzig, Germany, 1880, p. 366–371.Google Scholar
  21. Smith LDS, Hobbs G. Genus III. Clostridium Prazmowski 1880, 23. In: Buchanan RE, Gibbons NE (eds), Bergey’s Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 551–572.Google Scholar
  22. McClung LS, McCoy E. Genus II. Clostridium Prazmowski 1880. In: Breed RS, Murray EGD, Smith NR (eds), Bergey’s Manual of Determinative Bacteriology, Seventh Edition, The Williams and Wilkins Co., Baltimore, 1957, p. 634–693.Google Scholar
  23. McClung LS, McCoy E. (1957) Genus I. Clostridium Prazmovski 1880. Bergey’s Manual of Determinative Bacteriology. Baltimore: Williams and Wilkins. pp. 634–693.Google Scholar
  24. Ng H, Vaughn RH. Clostridium rubrum sp. n. and other pectinolytic clostridia from soil. J Bacteriol 1963; 85:1104–1113. PubMedPubMed CentralPubMedGoogle Scholar
  25. Drasar BS, Goddard P, Heaton S, Peach S, West B. Clostridia isolated from faeces. J Med Microbiol 1976; 9:63–71. PubMed http://dx.doi.org/10.1099/00222615-9-1-63View ArticlePubMedGoogle Scholar
  26. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed http://dx.doi.org/10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  27. Woo PCY. Clostridium bacteraemia characterised by 16S ribosomal RNA gene sequencing. J Clin Pathol 2005; 58:301–307. PubMed http://dx.doi.org/10.1136/jcp.2004.022830PubMed CentralView ArticlePubMedGoogle Scholar
  28. Bergey’s manual of systematic bacteriology: Volume Three: The Firmicutes (2009). 2nd ed. New York, NY: Springer.
  29. Duncan SH, Louis P, Flint HJ. Lactate-Utilizing Bacteria, Isolated from Human Feces, That Produce Butyrate as a Major Fermentation Product. Appl Environ Microbiol 2004; 70:5810–5817. PubMed http://dx.doi.org/10.1128/AEM.70.10.5810-5817.2004PubMed CentralView ArticlePubMedGoogle Scholar
  30. Antranikian G, Friese C, Quentmeier A, Hippe H, Gottschalk G. Distribution of the ability for citrate utilization amongst Clostridia. Arch Microbiol 1984; 138:179–182. http://dx.doi.org/10.1007/BF00402115View ArticleGoogle Scholar
  31. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed http://dx.doi.org/10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  32. Warnick Thomas A. Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. Int J Syst Evol Microbiol 2002; 52:1155–1160. PubMed http://dx.doi.org/10.1099/ijs.0.02125-0View ArticlePubMedGoogle Scholar
  33. Bennett S. Solexa, Inc. Pharmacogenomics 2004; 5:433–438. PubMed http://dx.doi.org/10.1517/14622416.5.4.433View ArticlePubMedGoogle Scholar
  34. Mingkun L, Copeland A, Han J. (2011) DUK. Walnut Creek, CA, USA: JGI.Google Scholar
  35. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 2010; 108:1513–1518. PubMed http://dx.doi.org/10.1073/pnas.1017351108PubMed CentralView ArticlePubMedGoogle Scholar
  36. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119PubMed CentralView ArticlePubMedGoogle Scholar
  37. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 0955–0964.View ArticleGoogle Scholar
  38. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188–7196. PubMed http://dx.doi.org/10.1093/nar/gkm864PubMed CentralView ArticlePubMedGoogle Scholar
  39. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009; 25:1335–1337. PubMed http://dx.doi.org/10.1093/bioinformatics/btp157PubMed CentralView ArticlePubMedGoogle Scholar
  40. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 2011; 40:D115–D122 PubMed http://dx.doi.org/10.1093/nar/gkr1044PubMed CentralView ArticleGoogle Scholar
  41. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar
  42. Cantarel BL. Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 2009; 37:D233–D238. PubMed http://dx.doi.org/10.1093/nar/gkn663PubMed CentralView ArticlePubMedGoogle Scholar
  43. Jojima T, Omumasaba CA, Inui M, Yukawa H. Sugar transporters in efficient utilization of mixed sugar substrates: current knowledge and outlook. Appl Microbiol Biotechnol 2009; 85:471–480. PubMed http://dx.doi.org/10.1007/s00253-009-2292-1View ArticleGoogle Scholar
  44. Stülke J, Hillen W. Regulation of carbon catabolism in Bacillus species. Annu Rev Microbiol 2000; 54:849–880. PubMed http://dx.doi.org/10.1146/annurev.micro.54.1.849View ArticlePubMedGoogle Scholar
  45. Saier MH. Families of transmembrane sugar transport proteins. Mol Microbiol 2000; 35:699–710. PubMed http://dx.doi.org/10.1046/j.1365-2958.2000.01759.xView ArticlePubMedGoogle Scholar
  46. Brückner R, Titgemeyer F. Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol Lett 2002; 209:141–148. PubMed http://dx.doi.org/10.1016/S0378-1097(02)00559-1View ArticlePubMedGoogle Scholar
  47. Forward JA, Behrendt MC, Wyborn NR, Cross R, Kelly DJ. TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria. J Bacteriol 1997; 179:5482–5493. PubMedPubMed CentralPubMedGoogle Scholar
  48. Bott M. Anaerobic citrate metabolism and its regulation in enterobacteria. Arch Microbiol 1997; 167:78–88. http://dx.doi.org/10.1007/s002030050419View ArticleGoogle Scholar
  49. Walther R, Hippe H, Gottschalk G. Citrate, a specific substrate for the isolation of Clostridium sphenoides. Appl Environ Microbiol 1977; 33:955–962. PubMedPubMed CentralPubMedGoogle Scholar
  50. Schneider K, Dimroth P, Bott M. Biosynthesis of the Prosthetic Group of Citrate Lyase †. Biochemistry (Mosc) 2000; 39:9438–9450. PubMed http://dx.doi.org/10.1021/bi000401rView ArticleGoogle Scholar
  51. Brocker M, Schaffer S, Mack C, Bott M. Citrate Utilization by Corynebacterium glutamicum Is Controlled by the CitAB Two-Component System through Positive Regulation of the Citrate Transport Genes citH and tctCBA. J Bacteriol 2009; 191:3869–3880. PubMed http://dx.doi.org/10.1128/JB.00113-09PubMed CentralView ArticlePubMedGoogle Scholar
  52. Leschine SB, Holwell K, Canale-Parola E. Nitrogen fixation by anaerobic cellulolytic bacteria. Science 1988; 242:1157–1159. PubMed http://dx.doi.org/10.1126/science.242.4882.1157View ArticlePubMedGoogle Scholar
  53. Chen JS, Toth J, Kasap M. Nitrogen-fixation genes and nitrogenase activity inClostridium acetobutylicum and Clostridium beijerinckii. J Ind Microbiol Biotechnol 2001; 27:281–286. PubMed http://dx.doi.org/10.1038/sj.jim.7000083View ArticlePubMedGoogle Scholar
  54. Dos Santos PC, Fang Z, Mason SW, Setubal JC, Dixon R. Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genomics 2012; 13:162. PubMed http://dx.doi.org/10.1186/1471-2164-13-162PubMed CentralView ArticlePubMedGoogle Scholar
  55. Yeates TO, Thompson MC, Bobik TA. The protein shells of bacterial microcompartment organelles. Curr Opin Struct Biol 2011; 21:223–231. PubMed http://dx.doi.org/10.1016/j.sbi.2011.01.006PubMed CentralView ArticlePubMedGoogle Scholar
  56. Kerfeld CA, Heinhorst S, Cannon GC. Bacterial Microcompartments. Annu Rev Microbiol 2010; 64:391–408. PubMed http://dx.doi.org/10.1146/annurev.micro.112408.134211View ArticlePubMedGoogle Scholar
  57. Garsin DA. Ethanolamine utilization in bacterial pathogens: roles and regulation. Nat Rev Microbiol 2010; 8:290–295. PubMed http://dx.doi.org/10.1038/nrmicro2334PubMed CentralView ArticlePubMedGoogle Scholar
  58. Petit E, LaTouf WG, Coppi MV, Warnick TA, Currie D, Romashko I, Deshpande S, Haas K, Alvelo-Maurosa JG, Wardman C, et al. Involvement of a Bacterial Microcompartment in the Metabolism of Fucose and Rhamnose by Clostridium phytofermentans. PLoS ONE 2013; 8:e54337. PubMed http://dx.doi.org/10.1371/journal.pone.0054337PubMed CentralView ArticlePubMedGoogle Scholar
  59. Scott KP, Martin JC, Campbell G, Mayer CD, Flint HJ. Whole-Genome Transcription Profiling Reveals Genes Up-Regulated by Growth on Fucose in the Human Gut Bacterium “Roseburia inulinivorans.”. J Bacteriol 2006; 188:4340–4349. PubMed http://dx.doi.org/10.1128/JB.00137-06PubMed CentralView ArticlePubMedGoogle Scholar
  60. Jorda J, Lopez D, Wheatley NM, Yeates TO. Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria. Protein Sci 2013; 22:179–195. PubMed http://dx.doi.org/10.1002/pro.2196PubMed CentralView ArticlePubMedGoogle Scholar
  61. Craciun S, Balskus EP. Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proc Natl Acad Sci USA 2012; 109:21307–21312. PubMed http://dx.doi.org/10.1073/pnas.1215689109PubMed CentralView ArticlePubMedGoogle Scholar
  62. Crawford RL, McCoy E, Harkin JM, Kirk TK, Obst JR. Degradation of methoxylated benzoic acids by a Nocardia from a lignin-rich environment: significance to lignin degradation and effect of chloro substituents. Appl Microbiol 1973; 26:176–184. PubMedPubMed CentralPubMedGoogle Scholar
  63. Stackebrandt E, Rainey FA. (1997) Phylogenic relationships. In: Rood JI, McClane BA, Songer JG, Titball RW, editors. The Clostridia: Molecular Biology and Pathogenesis. New York, NY: Academic Press. p. 533.Google Scholar
  64. Lawson PA, Llop-Perez P, Hutson RA, Hippe H, Collins MD. Towards a phylogeny of the clostridia based on 16S rRNA sequences. FEMS Microbiol Lett 1993; 113:87–92. PubMed http://dx.doi.org/10.1111/j.1574-6968.1993.tb06493.xView ArticlePubMedGoogle Scholar

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