Genome analysis of Paenibacillus polymyxa A18 gives insights into the features associated with its adaptation to the termite gut environment

Abstract

Paenibacillus polymyxa A18 was isolated from termite gut and was identified as a potential cellulase and hemicellulase producer in our previous study. Considering that members belonging to genus Paenibacillus are mostly free-living in soil, we investigated here the essential genetic features that helped P. polymyxa A18 to survive in gut environment. Genome sequencing and analysis identified 4608 coding sequences along with several elements of horizontal gene transfer, insertion sequences, transposases and integrated phages, which add to its genetic diversity. Many genes coding for carbohydrate-active enzymes, including the enzymes responsible for woody biomass hydrolysis in termite gut, were identified in P. polymyxa A18 genome. Further, a series of proteins conferring resistance to 11 antibiotics and responsible for production of 4 antibiotics were also found to be encoded, indicating selective advantage for growth and colonization in the gut environment. To further identify genomic regions unique to this strain, a BLAST-based comparative analysis with the sequenced genomes of 47 members belonging to genus Paenibacillus was carried out. Unique regions coding for nucleic acid modifying enzymes like CRISPR/Cas and Type I Restriction-Modification enzymes were identified in P. polymyxa A18 genome suggesting the presence of defense mechanism to combat viral infections in the gut. In addition, genes responsible for the formation of biofilms, such as Type IV pili and adhesins, which might be assisting P. polymyxa A18 in colonizing the gut were also identified in its genome. In situ colonization experiment further confirmed the ability of P. polymyxa A18 to colonize the gut of termite.

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

“…These regions may encode numerous beneficial traits for bacteria and thus have an influence on better adaptation of microorganisms to changing environmental conditions. Due to the gene content, these regions can be divided into pathogenicity, metabolic, fitness, symbiosis and resistance islands and can be distinguished from the host genome based on different nucleotide compositions, including IS fragments, anomalous GC content, transposons and tRNA genes 37,38 . To evaluate the genetic diversity of E. aerogenes LU2, the presence of GIs acquired through HGT was identified using the IslandViewer 4 platform and the IslandPath-DIMOB, SIGI-HMM, and IslandPick prediction methods (Additional file 1) 39 .…”

Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events

“…The list of genomes is shown in Supplementary Table S1 . The nearly perfect correspondence of the reconstructed (the current figure) tree and the species tree (Figure 2 in [ 26 ]) is a well-known property of the vertically inherited sequences [ 27 ] and suggests the absence of horizontal gene transfer events in the set of studied sequences ( Figure 1 ).…”

Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil

“…The complete genome size of isolate YH-JAE5 T was 6 476 225 bp with a G+C content of 47.4 mol%. The G+C content of isolate YH-JAE5 T is within the range of the genus Paenibacillus [47]. The G+C contents of the most closely related Paenibacillus strains were 52.8 mol% for P. chibensis KCTC 3758 T [48], 50.9 mol% for P. solani DSM 100999 T [18] and 51.6 mol% for P. cookii KCTC 3999 T [49], showing that the G+C content of YH-JAE5 T was lower than those of the related species of the genus Paenibacillus.…”

“…The complete genome size of isolate YH-JAE5 T was 6 476 225 bp with a G+C content of 47.4 mol%. The G+C content of isolate YH-JAE5 T is within the range of the genus Paenibacillus [47]. The G+C contents of the most closely related Paenibacillus strains were 52.8 mol% for P.…”