Complete genome sequence of Paludibacter propionicigenes type strain (WB4T)

Gronow, Sabine; Munk, Christine; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan‐Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia D.; Brambilla, Evelyne; Rohde, Manfred; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter

doi:10.4056/sigs.1503846

Cited by 31 publications

(13 citation statements)

References 22 publications

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“…1 ). This separation has also been demonstrated previously using analysis of 16S rDNA gene sequences ( Fournier et al 2001 ; Summanen et al 2009 , 2005 ; Gronow et al 2011 ). The nonoral isolates (isolated from a skin abscess, leg ulcer, and bovine rumen) have been described as opportunistic pathogens, with their presence reported in clinical infections in a number of studies ( Finegold et al 2004 ; Summanen et al 2005 ; Sweeney et al 2009 ).…”

Section: Discussionsupporting

confidence: 80%

Comparative Genomics of the GenusPorphyromonasIdentifies Adaptations for Heme Synthesis within the Prevalent Canine Oral SpeciesPorphyromonas cangingivalis

O’Flynn¹,

Deusch²,

Darling

et al. 2015

Genome Biol Evol

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Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions characterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to synthesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. Other pathway differences such as the ability to synthesize siroheme and vitamin B12 point to enhanced metabolic flexibility for P. cangingivalis, which may underlie its prevalence in the canine oral cavity.

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Section: Discussionsupporting

confidence: 80%

Comparative Genomics of the GenusPorphyromonasIdentifies Adaptations for Heme Synthesis within the Prevalent Canine Oral SpeciesPorphyromonas cangingivalis

O’Flynn¹,

Deusch²,

Darling

et al. 2015

Genome Biol Evol

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“…One gene designated as cpheE1 was always present and encodes a canonical single domain cyanophycinase. The other gene ( cphE2 ), which was missing in the genome of Paludibacter propionicigenes DSM 17365 T (Gronow et al ., ), contains an additional C‐terminal region that seems to have a function in the transport and anchoring of the protein to the outer membrane (in most cases a Por secretion system domain). Interestingly, in several cases the cyanophycinase domain of the cphE2 gene was highly divergent to typical cyanophycinases, which could indicate a relaxed selection pressure on the enzymatic function of the CphE2 protein.…”

Section: Resultsmentioning

confidence: 99%

Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria

Hania

Joseph

Bunk

et al. 2017

Environmental Microbiology

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“…To identify the likely location of nitrogen fixation, nitrogenase gene expression was quantified by using nifH-qPCR. This demonstrated that nifH expression was highest in the AHG (27-fold higher than the FG; Table 2), with the predominant nifH transcript sequences related to the Ni-Fe nitrogenase of the member of the Porphyromonadales, P. propionicigenes (Gronow et al, 2011) as well as the Ni-Fe nitrogenase of Clostridiales member, C. lentocellum, a cellulolytic N 2 -fixing bacterium (Leschine and Canale-Parola, 1989;Leschine, 1995). NifH expression results confirmed our hypothesis of microbial compositional and functional segregation because of differential physiological conditions, that is, variation in O 2 concentrations at each gut region.…”

Section: Discussionmentioning

confidence: 99%

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut ofOdontotaenius disjunctus

et al. 2013

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Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by 15 N 2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni-Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N 2 that is important for this beetle to subsist on woody biomass.

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Complete genome sequence of Paludibacter propionicigenes type strain (WB4T)

Cited by 31 publications

References 22 publications

Comparative Genomics of the GenusPorphyromonasIdentifies Adaptations for Heme Synthesis within the Prevalent Canine Oral SpeciesPorphyromonas cangingivalis

Comparative Genomics of the GenusPorphyromonasIdentifies Adaptations for Heme Synthesis within the Prevalent Canine Oral SpeciesPorphyromonas cangingivalis

Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut ofOdontotaenius disjunctus

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