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Caldibacillus debilis strains GB1 and Tf display distinct phenotypes. Caldibacillus debilis GB1 is capable of anaerobic growth and can synthesize ethanol while C. debilis Tf cannot. Comparison of the GB1 and Tf genome sequences revealed that the genomes were highly similar in gene content and showed a high level of synteny. At the genome scale, there were several large sections of DNA that appeared to be from lateral gene transfer into the GB1 genome. Tf did have unique genetic content but at a much smaller scale: 300 genes in Tf verses 857 genes in GB1 that matched at ≤90% sequence similarity. Gene complement and copy number of genes for the glycolysis, tricarboxylic acid cycle, and electron transport chain pathways were identical in both strains. While Tf is an obligate aerobe, it possesses the gene complement for an anaerobic lifestyle ( ldh , ak , pta , adhE , pfl ). As a species, other strains of C. debilis should be expected to have the potential for anaerobic growth. Assaying the whole cell lysate for alcohol dehydrogenase activity revealed an approximately 2-fold increase in the enzymatic activity in GB1 when compared with Tf.

This study characterizes a cryptic (pro)phage-related sequence within the Caldibacillus debilis GB1 genome, designated CBP1.CBP1 is a Siphoviridae-like genome highly related to GBVS1 from Geobacillus sp. 6k51. The CBP1genome is a 37,315 bp region containing 69 putative ORFs with a GC content of 42% flanked on both sides by host DNA integrated into the main bacterial chromosome (contig 16). Bioinformatic analyses identified cassettes of genes within the CBP1 genome that were similar in function, yet distinct in sequence, from genes previously identified in GBVS1. All of CBP1 genes had less than 60% amino acid sequence identity with GBVS1by tBLASTx, with the exception of the TMP repeat gene. CBP1 possessed all the necessary genes to undergo a temperate/lytic phage life cycle, including excision, replication, structural genes, DNA packaging, and cell lyses. Proteomic analysis of CBP1 revealed the expression of 5 proteins. One of the expressed proteins was a transcriptional regulator protein homologous to the bacteriophage λ repressor protein (cI) expressed in high amounts from the CBP1 region, consistent with a lysogenic phage in a repressed state. The CBP1 protein expression profile during host growth provides unique insight into thermophilic Siphoviridae-like phages in the repressed state within their host cells.

Caldibacillus debilis GB1 is a facultative anaerobe isolated from a thermophilic aero-tolerant cellulolytic enrichment culture. There is a lack of representative proteomes of facultative anaerobic thermophilic Bacillaceae, exploring aerobic/anaerobic expression. The C. debilis GB1 genome was sequenced and annotated, and the proteome characterized under aerobic and anaerobic conditions while grown on cellobiose. The draft sequence of C. debilis GB1 contains a 3,340,752 bp chromosome and a 5,386 bp plasmid distributed over 49 contigs. Two-dimensional liquid chromatography mass spectrometry/mass spectrometry was used with Isobaric Tags for Relative and Absolute Quantification (iTRAQ) to compare protein expression profiles, focusing on energy production and conversion pathways. Under aerobic conditions, proteins in glycolysis and pyruvate fermentation pathways were down-regulated. Simultaneously, proteins within the tricarboxylic acid cycle, pyruvate dehydrogenase, the electron transport chain, and oxygen scavenging pathways showed increased amounts. Under anaerobic conditions, protein levels in fermentation pathways were consistent with the generated end-products: formate, acetate, ethanol, lactate, and CO 2 . Under aerobic conditions CO 2 and acetate production was consistent with incomplete respiration. Through a direct comparison with gene expression profiles from Escherichia coli, we show that global regulation of core metabolism pathways is similar in thermophilic and mesophilic facultative anaerobes of the Phylum Proteobacteria and Firmicutes., (Copyright © 2017 Elsevier GmbH. All rights reserved.)