Extra-abdominal infections caused by Comamonas kerstersii: Case report.

RATIONALE: Comamonas kerstersii mainly causes intra-abdominal infections with favorable outcomes due to high antibiotic susceptibility. We report the first case of pneumonia caused by C Kerstersii, which promoted patient death, and a second urinary tract infection by C Kerstersii with extensive drug resistance. PATIENT CONCERNS: A 46-year-old male (Case 1) with craniocerebral injury underwent emergency decompressive craniectomy, but his condition deteriorated further and presented with discontinuous fever, small moist rales on both lungs, and respiratory failure. Retrospective average nucleotide identity (ANI) analysis of the genomic sequence of the sputum isolate identified it as C Kerstersii 12322-1, antimicrobial susceptibility testing (AST) revealed that it was sensitive to 18 of 21 tested antibiotics.An 82-year-old male (Case 2) with hypertrophic prostate experienced gradual obstruction during urination, and a urine test revealed WBC ++. Retrospective ANI analysis of the urine isolate identified it as C Kerstersii 121606, which was resistant to 18 of 21 tested antibiotics. DIAGNOSES: Case 1 was diagnosed empirically as pneumonia caused by C Kerstersii strain 12322-1 secondary to craniocerebral injury and confirmed by retrospective ANI analysis; case 2 was diagnosed empirically as urinary infection secondary to prostate hyperplasia caused by C Kerstersii strain 121606 confirmed by the retrospective ANI analysis. INTERVENTIONS: Case 1 was administered cefoxitin, cefodizime, imipenem-cilastatin sodium, and underwent comprehensive salvage management. Case 2 was administered doxycycline alone. OUTCOMES: Case 1 died partially because of untimely identification of the responsible bacteria-12322-1. Case 2 was cured even 121606 exhibited an extensive drug resistance feature. LESSONS: Except for intra-abdominal infections with good prognosis, we verified that C Kerstersii could also cause extra-abdominal infections, such as the first pneumonia case and urinary infection. It could promote patient death; actual infections were underestimated due to identification difficulties, posing a health threat due to the presence of extensive drug resistance.

Comamonas resistens sp. nov. and Pseudomonas triclosanedens sp. nov., two members of the phylum Pseudomonadota isolated from the wastewater treatment system of a pharmaceutical factory.

Five strains of two novel species were isolated from the wastewater treatment systems of a pharmaceutical factory located in Zhejiang province, PR China. Strains ZM22T and Y6 were identified as belonging to a potential novel species of the genus Comamonas, whereas strains ZM23T, ZM24 and ZM25 were identified as belonging to a novel species of the genus Pseudomonas. These strains were characterized by polyphasic approaches including 16S rRNA gene analysis, multi-locus sequence analysis, average nucleotide identity (ANI), in silico DNA-DNA hybridization (isDDH), physiological and biochemical tests, as well as chemotaxonomic analysis. Genome-based phylogenetic analysis further confirmed that strains ZM22T and Y6 form a distinct clade closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T. Strains ZM23T, ZM24 and ZM25 were grouped as a separate clade closely related to Pseudomonas nitroreducens DSM 14399T and Pseudomonas nicosulfuronedens LAM1902T. The orthoANI and isDDH results indicated that strains ZM22T and Y6 belong to the same species. In addition, genomic DNA fingerprinting demonstrated that these strains do not originate from a single clone. The same results were observed for strains ZM23T, ZM24 and ZM25. Strains ZM22T and Y6 were resistant to multiple antibiotics, whereas strains ZM23T, ZM24 and ZM25 were able to degrade an emerging pollutant, triclosan. The phylogenetic, physiological and biochemical characteristics, as well as chemotaxonomy, allowed these strains to be distinguished from their genus, and we therefore propose the names Comamonas resistens sp. nov. (type strain ZM22=MCCC 1K08496T=KCTC 82561T) and Pseudomonas triclosanedens sp. nov. (type strain ZM23T=MCCC 1K08497T=JCM 36056T), respectively.

Comamonas endophytica sp. nov., a novel indole acetic acid producing endophyte isolated from bamboo in China.

Two novel indole acetic acid-producing strains, 5MLIRT and D4N7, were isolated from Indosasa shibataeoides in Yongzhou, Hunan province, and Phyllostachys edulis in Hangzhou, Zhejiang province, respectively. Based on their 16S rRNA sequences, strains 5MLIRT and D4N7 were closely related to Comamonas antarcticus 16-35-5T (98.4 % sequence similarity), and the results of 92-core gene phylogenetic trees showed that strains 5MLIRT and D4N7 formed a phylogenetic lineage within the clade comprising Comamonas species. The complete genome size of strain 5MLIRT was 4.49 Mb including two plasmids, and the DNA G+C content was 66.5 mol%. The draft genome of strain D4N7 was 4.26 Mb with 66.7 mol% G+C content. The average nucleotide identity and digital DNA-DNA hybridization values among strain 5MLIRT and species in the genus Comamonas were all below the species delineation threshold. The colonies of strain 5MLIRT and D4N7 were circular with regular margins, convex, pale yellow and 1.0-2.0 mm in diameter when incubated at 30 °C for 3 days. Strains 5MLIRT and D4N7 grew optimally at 30 °C, pH 7.0 and 1.0 % NaCl. The respiratory isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Polyphasic analyses indicated that strains 5MLIRT and D4N7 could be distinguished from related validly named Comamonas species and represent a novel species of the genus Comamonas, for which the name Comamonas endophytica sp. nov. is proposed. The type strain is 5MLIRT (=ACCC 62069T=GDMCC 1.2958T=JCM 35331T).

Regulating mechanism of denitrifier Comamonas sp. YSF15 in response to carbon deficiency: Based on carbon/nitrogen functions and bioaggregation.

There is an urgent demand to investigate mechanisms for the improvement of denitrification in carbon-deficient environment, which will effectively reduce the eutrophication in water bodies polluted by nitrate. In this study, denitrifying bacterium Comamonas sp. YSF15 was used to explore the differences in different carbon source concentrations, with the complete genome, metabolomics, and other detecting methods. Results showed that strain YSF15 was able to achieve efficient denitrification, with complete pathways for denitrification and central carbon metabolism. The carbon deficiency prompted the bacteria to use extracellular amino acid-like metabolites initially, to alleviate inhibition and maintain bioactivity, which also facilitated glycogen storage. The biogenic inhibitors (tautomycin, navitoclax, and glufosinate) at extremely low level potentially favored the competitiveness and intraspecific utilization of extracellular polysaccharides (PS). Optimal solutions for bioaggregation in carbon-deficient condition are achieved by regulating the hydrophobicity, and hydrogen bond in extracellular metabolites. The strategy contributes to the maintenance of bioactivity and adaptation to carbon deficiency. Overall, this study provides a new perspective on understanding the denitrification strategies in carbon-deficient environment, and helps to improve the nitrate removal in low-carbon wastewater treatment.

Molecular mechanism underlying high-affinity terephthalate binding and conformational change of TBP from Ideonella sakaiensis.

Ideonella sakaiensis is the bacterium that can survive by degrading polyethylene terephthalate (PET) plastic, and terephthalic acid (TPA) binding protein (IsTBP) is an essential periplasmic protein for uptake of TPA into the cytosol for complete degradation of PET. Here, we demonstrated that IsTBP has remarkably high specificity for TPA among 33 monophenolic compounds and two 1,6-dicarboxylic acids tested. Structural comparisons with 6-carboxylic acid binding protein (RpAdpC) and TBP from Comamonas sp. E6 (CsTphC) revealed the key structural features that contribute to high TPA specificity and affinity of IsTBP. We also elucidated the molecular mechanism underlying the conformational change upon TPA binding. In addition, we developed the IsTBP variant with enhanced TPA sensitivity, which can be expanded for the use of TBP as a biosensor for PET degradation.

A new class A beta-lactamase gene blaCAE-1 coexists with blaAFM-1 in a novel untypable plasmid in Comamonas aquatica.

Antimicrobial resistance, especially carbapenem resistance, poses a serious threat to global public health. Here, a carbapenem-resistant Comamonas aquatica isolate SCLZS63 was recovered from hospital sewage. Whole-genome sequencing showed that SCLZS63 has a 4,048,791-bp circular chromosome and three plasmids. The carbapenemase gene blaAFM-1 is located on the 143,067-bp untypable plasmid p1_SCLZS63, which is a novel type of plasmid with two multidrug-resistant (MDR) regions. Notably, a novel class A serine ß-lactamase gene, blaCAE-1, coexists with blaAFM-1 in the mosaic MDR2 region. Cloning assay showed that CAE-1 confers resistance to ampicillin, piperacillin, cefazolin, cefuroxime, and ceftriaxone, and elevates the MIC of ampicillin-sulbactam two-fold in Escherichia coli DH5α, suggesting that CAE-1 functions as a broad-spectrum ß-lactamase. Amino acid sequences analysis suggested that blaCAE-1 may originate from Comamonadaceae. The blaAFM-1 in p1_SCLZS63 is located in a conserved structure of ISCR29-ΔgroL-blaAFM-1-ble-ΔtrpF-ΔISCR27-msrB-msrA-yfcG-corA. Comprehensive analysis of the blaAFM-bearing sequences revealed important roles of ISCR29 and ΔISCR27 in the mobilization and truncation of the core module of blaAFM alleles, respectively. The diverse passenger contents of class 1 integrons flanking the blaAFM core module make the complexity of genetic contexts for blaAFM. In conclusion, this study reveals that Comamonas may act as an important reservoir for antibiotics-resistance genes and plasmids in the environment. Continuous monitoring for the environmental emergence of antimicrobial-resistant bacteria is needed to control the spread of antimicrobial resistance.

Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism.

Critical to a sustainable energy future are microbial platforms that can process aromatic carbons from the largely untapped reservoir of lignin and plastic feedstocks. Comamonas species present promising bacterial candidates for such platforms because they can use a range of natural and xenobiotic aromatic compounds and often possess innate genetic constraints that avoid competition with sugars. However, the metabolic reactions of these species are underexplored, and the regulatory mechanisms are unknown. Here we identify multilevel regulation in the conversion of lignin-related natural aromatic compounds, 4-hydroxybenzoate and vanillate, and the plastics-related xenobiotic aromatic compound, terephthalate, in Comamonas testosteroni KF-1. Transcription-level regulation controls initial catabolism and cleavage, but metabolite-level thermodynamic regulation governs fluxes in central carbon metabolism. Quantitative 13C mapping of tricarboxylic acid cycle and cataplerotic reactions elucidates key carbon routing not evident from enzyme abundance changes. This scheme of transcriptional activation coupled with metabolic fine-tuning challenges outcome predictions during metabolic manipulations.

Sediment-isolated Comamonas terrigena strain HJ-2: a novel nitrate-dependent ferrous-oxidizing bacterium with multifunction on pollutant transformation.

Microbially driven Fe(II) oxidation is vital for Fe-cycling processes. In the present study, a novel strain of nitrate-dependent Fe-oxidizing bacteria (FOB) was isolated from the riparian zone sediment of the Hanjiang River, China. It was identified as Comamonas terrigena strain HJ-2. The strain HJ-2 oxidized 2.80 mmol l-1 Fe(II) within 144 h to form Fe(III)/Fe(II) complex on the cell surface using 1.63 mmol l-1 nitrate as an electron acceptor. The formed nitrite from nitrate reduction chemically oxidized Fe(II). Surprisingly, this strain also reduced nitrilotriacetic iron to form 0.5 mmol l-1 Fe(II) in 120 h in anaerobic conditions primarily mediated by the NADH flavin oxidoreductase. Besides, the strain completely reduced 0.18 mmol l-1 nitrobenzene to aniline in 24 days and 15.6 µmol l-1 arsenate to arsenite in 7 days due to the existence of nitro and arsenate reductases. However, the Fe(II) inhibited the reduction of nitrate, nitrobenzene, and arsenate, possibly due to the impeding of transport of the solutes through the membrane or the synthesis of the related enzymes. These results provide new knowledge about the Fe(II)-cycling and the fate of some pollutants in the riparian zone. It also informed that some bacteria have universal functions on elements and contaminants transformation.

An Ultra-Sensitive Comamonas thiooxidans Biosensor for the Rapid Detection of Enzymatic Polyethylene Terephthalate (PET) Degradation.

Polyethylene terephthalate (PET) is a prevalent synthetic polymer that is known to contaminate marine and terrestrial environments. Currently, only a limited number of PET-active microorganisms and enzymes (PETases) are known. This is in part linked to the lack of highly sensitive function-based screening assays for PET-active enzymes. Here, we report on the construction of a fluorescent biosensor based on Comamonas thiooxidans strain S23. C. thiooxidans S23 transports and metabolizes TPA, one of the main breakdown products of PET, using a specific tripartite tricarboxylate transporter (TTT) and various mono- and dioxygenases encoded in its genome in a conserved operon ranging from tphC-tphA1. TphR, an IclR-type transcriptional regulator is found upstream of the tphC-tphA1 cluster where TPA induces transcription of tphC-tphA1 up to 88-fold in exponentially growing cells. In the present study, we show that the C. thiooxidans S23 wild-type strain, carrying the sfGFP gene fused to the tphC promoter, senses TPA at concentrations as low as 10 µM. Moreover, a deletion mutant lacking the catabolic genes involved in TPA degradation thphA2-A1 (ΔtphA2A3BA1) is up to 10,000-fold more sensitive and detects TPA concentrations in the nanomolar range. This is, to our knowledge, the most sensitive reporter strain for TPA and we demonstrate that it can be used for the detection of enzymatic PET breakdown products. IMPORTANCE Plastics and microplastics accumulate in all ecological niches. The construction of more sensitive biosensors allows to monitor and screen potential PET degradation in natural environments and industrial samples. These strains will also be a valuable tool for functional screenings of novel PETase candidates and variants or monitoring of PET recycling processes using biocatalysts. Thereby they help us to enrich the known biodiversity and efficiency of PET degrading organisms and enzymes and understand their contribution to environmental plastic degradation.

A Coculture of Enterobacter and Comamonas Species Reduces Cadmium Accumulation in Rice.

The accumulation of cadmium (Cd) in plants is strongly impacted by soil microbes, but its mechanism remains poorly understood. Here, we report the mechanism of reduced Cd accumulation in rice by coculture of Enterobacter and Comamonas species. In pot experiments, inoculation with the coculture decreased Cd content in rice grain and increased the amount of nonbioavailable Cd in Cd-spiked soils. Fluorescence in situ hybridization and scanning electron microscopy detection showed that the coculture colonized in the rhizosphere and rice root vascular tissue and intercellular space. Soil metagenomics data showed that the coculture increased the abundance of sulfate reduction and biofilm formation genes and related bacterial species. Moreover, the coculture increased the content of organic matter, available nitrogen, and potassium and increased the activities of arylsulfatase, ß-galactosidase, phenoloxidase, arylamidase, urease, dehydrogenase, and peroxidase in soils. In subsequent rice transcriptomics assays, we found that the inoculation with coculture activated a hypersensitive response, defense-related induction, and mitogen-activated protein kinase signaling pathway in rice. Heterologous protein expression in yeast confirmed the function of four Cd-binding proteins (HIP28-1, HIP28-4, BCP2, and CID8), a Cd efflux protein (BCP1), and three Cd uptake proteins (COPT4, NRAM5, and HKT6) in rice. Succinic acid and phenylalanine were subsequently proved to inhibit rice divalent Cd [Cd(II)] uptake and activate Cd(II) efflux in rice roots. Thus, we propose a model that the coculture protects rice against Cd stress via Cd immobilization in soils and reducing Cd uptake in rice. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome-based analyses of the genus Acidovorax: proposal of the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the reclassification of Acidovorax antarcticus as Comamonas antarctica comb. nov. and emended description of the genus Acidovorax.

The genus Acidovorax is a genetically heterogeneous species clustering that comprises many environmental and plant-pathogenic taxa. To better understand the evolutionary relationships among the Acidovorax species, 22 available genome sequences of type strains including the genera Acidovorax and Comamonas were used to conduct the genome-based analyses. Three well-supported monophyletic clusters of the Acidovorax species were determined based on the phylogenomic tree reconstructed using core genes, while they were not grouped in the 16S rRNA gene-based phylogenetic tree. The species arrangements of the genus Acidovorax were further confirmed by the comparisons of the digital DNA-DNA hybridization and average nucleotide identity (ANI) values. The ANI, average amino acid identity, and the percentage of conserved proteins values among the inter-clusters were approximately 83, 81, and 61%, respectively, and thus were proposed as practical thresholds for genus delineation. Besides, Acidovorax antarcticus was much closer to members of the genus Comamonas rather than those of the genus Acidovorax based on the genome-based analysis. Taken together, we propose the division of the current genus Acidovorax into the emended genus Acidovorax and the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the transfer of Acidovorax antarcticus into the genus Comamonas as Comamonas antarctica comb. nov.

Quantitative proteomic analysis of the microbial degradation of 3-aminobenzoic acid by Comamonas sp. QT12.

A mab cluster associated with 3-aminobenzoic acid (3AB) degradation was identified in Comamonas sp. QT12. However, the cellular response of Comamonas sp. QT12 to 3-aminobenzoic acid remains unclear. In this study, label-free quantitative proteome analysis based on LC-MS/MS was used to study the protein expression difference of strain QT12 under the condition of using 3AB (3AB) and citric acid/ammonium chloride as substrates (3ABCon). A total of 2068 proteins were identified, of which 239 were significantly up-regulated in 3AB group, 124 were significantly down-regulated in 3AB group, 624 were expressed only in 3AB group, and 216 were expressed only in 3ABCon group in 3AB group. KEGG pathway analysis found that 83 pathways were up-regulated and 49 pathways were down-regulated, In GO analysis, 315 paths were up-regulated and 156 paths were down-regulated. There were 6 genes in the mab cluster that were only detected in the 3AB group.The mab cluster was found to be related to degradation of 3AB. By knockout, it was found that the growth rate of the mutant △orf7 and △orf9 were slowed down. HPLC results showed that the mutant △orf7 and △orf9 could still degrade 3AB, it was found that orf7, orf9 were not key genes about 3AB degradation and they could be replaced by other genes in strain QT12. These findings improve our understanding of the molecular mechanisms underlying the cellular response of 3AB degradation in Comamonas bacterium.

A young child with acute perforated appendicitis due to Comamonas kerstersii: a rare case report.

Comamonas species are rarely associated with human infections. Recent reports found that Comamonas kerstersii was associated with severe diseases such as abdominal infection and bacteremia. However, Comamonas kerstersii may be confused with Comamonas testosteroni using the automatic bacterial identification systems currently available. An 8-year-old boy who had a right iliac fossa pain and classic migration of pain at the temperature of 38.9°C. The positive strain of aerobic and anaerobic bottles of blood cultures was identified. The patient was diagnosed as acute peritonitis and perforated appendix with abdominal abscess. The bacterium was identified by routine methods, MALDI-TOF-MS. The patient was treated with exploratory laparotomy, appendectomy, tube drainage, and prescribing antibiotic treatment. The patient was discharged with complete recovery. The organisms were confirmed as Comamonas kerstersii by MALDI-TOFMS and a combination of the other results. Our findings suggest that Comamonas kerstersii infection occurs most often in association with perforated appendix and bacteremia. We presume that Comamonas kerstersii is an opportunistic pathogen or commensal with the digestive tract and appendix bacteria.

Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments.

Comamonas spp. are Gram-negative bacteria that catabolize a wide range of organic and inorganic substrates. Comamonas spp. are abundant in aquatic and soil environments, including wastewater, and can cause opportunistic infections in humans. Because of their potential in wastewater bioaugmentation and bioremediation strategies, the identification of Comamonas species harboring genes encoding carbapenemases and other clinically important antibiotic resistance genes warrant further investigation. Here, we present an analysis of 39 whole-genome sequences comprising three Comamonas species from aquatic environments in South Australia that were recovered on media supplemented with carbapenems. The analysis includes a detailed description of 33 Comamonas denitrificans isolates, some of which carried chromosomally acquired blaGES-5, blaOXA, and aminoglycoside resistance (aadA) genes located on putative genomic islands (GIs). All blaGES-5- and blaOXA-containing GIs appear to be unique to this Australian collection of C. denitrificans. Notably, most open reading frames (ORFs) within the GIs, including all antimicrobial resistance (AMR) genes, had adjacent attC sites, indicating that these ORFs are mobile gene cassettes. One C. denitrificans isolate carried an IncP-1 plasmid with genes involved in xenobiotic degradation and response to oxidative stress. Our assessment of the sequences highlights the very distant nature of C. denitrificans to the other Comamonas species and its apparent disposition to acquire antimicrobial resistance genes on putative genomic islands. IMPORTANCE Antimicrobial resistance (AMR) poses a global public health threat, and the increase in resistance to "last-resort drugs," such as carbapenems, is alarming. Wastewater has been flagged as a hot spot for AMR evolution. Comamonas spp. are among the most common bacteria in wastewater and play a role in its bioaugmentation. While the ability of Comamonas species to catabolize a wide range of organic and inorganic substrates is well documented, some species are also opportunistic pathogens. However, data regarding AMR in Comamonas spp. are limited. Here, through the genomic analyses of 39 carbapenem-resistant Comamonas isolates, we make several key observations, including the identification of a subset of C. denitrificans isolates that harbored genomic islands encoding carbapenemase blaGES-5 or extended-spectrum ß-lactamase blaOXA alleles. Given the importance of Comamonas species in potential wastewater bioaugmentation and bioremediation strategies, as well as their status as emerging pathogens, the acquisition of critically important antibiotic resistance genes on genomic islands warrants future monitoring.

The role of nitrogen metabolism on polyethylene biodegradation.

Polyethylene (PE) is the most widely used plastic and its accumulation on natural environments has reached alarming levels causing severe damage to wildlife and human health. Despite the significance of this global issue, little is known about specific metabolic mechanisms behind PE biodegradation-a promising and sustainable remediation method. Herein, we describe a novel role of nitrogen metabolism in the fragmentation and oxidation of PE mediated by biological production of NOx in three PE-degrading strains of Comamonas, Delftia, and Stenotrophomonas. Resultant nitrated PE fragments are assimilated and then metabolized by these bacteria in a process assisted by nitronate monooxygenases and nitroreductases to support microbial growth. Due to the conservation of nitrogen metabolism genes, we anticipate that this oxidative mechanism is potentially shared by other nitrifier and denitrifier microbes.

Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea.

A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34T, was isolated from Han River water in the Republic of Korea. Strain CJ34T grew optimally on tryptic soy agar at 30 °C and pH 7.0 in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequence showed that strain CJ34T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34T and two closely related type strains C. testosteroni ATCC 11996T and C. thiooxydans DSM 17888T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34T were C16 : 0, C16 : 1 ω6c and/or C16 : 1 ω7c and C18 : 1 ω6c and/or C18 : 1 ω7c. The predominant polar lipids of strain CJ34T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34T had a genome of 4.9 Mbp and the G+C content of the genomic DNA was 59.73 mol%. On the basis of the results of this polyphasic taxonomy study, strain CJ34T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34T (=KACC 22237T=JCM 34454T).

Structural basis of terephthalate recognition by solute binding protein TphC.

Biological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions.

Comamonas suwonensis sp. nov., isolated from stream water in the Republic of Korea.

A novel bacterial strain, EJ-4T, isolated from stream water collected at Seo-ho in Suwon, Republic of Korea, was characterized based on a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EJ-4T belonged to the genus Comamonas. The isolate is Gram-stain-negative, non-motile, aerobic, rod-shaped and forms pale yellow colonies on trypticase soy agar. The optimal growth of this strain was observed aerobically at 30 °C, pH 7 and 0.5 % NaCl. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 39.7 %) and C16 : 0 (32.0 %). The G+C content of strain EJ-4T was 58.4mol %. The average nucleotide identity and digital DNA-DNA hybridization values between strain EJ-4T and Comamoas testosteroni were 91.8 and 31.2 %, respectively. The major polar lipids detected in the isolate were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was ubiquinone-8. Based on the results of polyphasic taxonomic analysis of strain EJ-4T, we describe a novel species of the genus Comamonas, for which the name Comamonas suwonensis sp. nov. has been proposed, with EJ-4T (=KCTC 82074T=JCM 34179T=KEMB 1602-279T) as the type strain.

Genes Encoding Microbial Acyl Coenzyme A Binding Protein/Diazepam-Binding Inhibitor Orthologs Are Rare in the Human Gut Microbiome and Show No Links to Obesity.

Acyl coenzyme A (CoA) binding protein (ACBP), also called diazepam-binding inhibitor (DBI), is a phylogenetically conserved protein that is expressed by all eukaryotic species as well as by some bacteria. Since elevated ACBP/DBI levels play a major role in the inhibition of autophagy, increase in appetite, and enhanced lipid storage that accompany obesity, we wondered whether ACBP/DBI produced by the human microbiome might affect host weight. We found that the genomes of bacterial commensals rarely contain ACBP/DBI homologues, which are rather encoded by genomes of some pathogenic or environmental taxa that were not prevalent in human feces. Exhaustive bioinformatic analyses of 1,899 gut samples from healthy individuals refuted the hypothesis that bacterial ACBP/DBI might affect the body mass index (BMI) in a physiological context. Thus, the physiological regulation of BMI is unlikely to be affected by microbial ACBP/DBI-like proteins. However, at the speculative level, it remains possible that ACBP/DBI produced by potential pathogenic bacteria might enhance their virulence by inhibiting autophagy and hence subverting innate immune responses. IMPORTANCE Acyl coenzyme A (CoA) binding protein (ACBP) can be encoded by several organisms across the domains of life, including microbes, and has shown to play major roles in human metabolic processes. However, little is known about its presence in the human gut microbiome and whether its microbial counterpart could also play a role in human metabolism. In the present study, we found that microbial ACBP/DBI sequences were rarely present in the gut microbiome across multiple metagenomic data sets. Microbes that carried ACBP/DBI in the human gut microbiome included Saccharomyces cerevisiae, Lautropia mirabilis, and Comamonas kerstersii, but these microorganisms were not associated with body mass index, further indicating an unconvincing role for microbial ACBP/DBI in human metabolism.

First report of urinary tract infection caused by Comamonas kerstersii in a goat.

BACKGROUND: Comamonas kerstersii is rarely associated with infections in humans and has never been reported in animals until now. CASE PRESENTATION: Herein, we describe a case of urinary tract infection caused by C. kerstersii in a young goat. A seven-month-old male goat showed lethargy, generalised weakness and anorexia and in the last hours before its death, severe depression, slight abdominal distention, ruminal stasis, and sternal recumbency. Grossly, multifocal haemorrhages in different organs and tissues, subcutaneous oedema and hydrocele, serous fluid with scattered fibrin deposition on the serosa of the abdominal organs and severe pyelonephritis with multifocal renal infarction were detected. Histopathological examination confirmed severe chronic active pyelonephritis with renal infarcts, multi-organ vasculitis and thrombosis suggestive of an infectious diseases of bacterial origin. The bacterium was identified using routine methods, matrix assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), and sequencing of the gyrB gene. CONCLUSIONS: To the best of our knowledge, this is the first report of C. kerstersii infection in animals (goat). Our findings support the possibility of C. kerstersii isolation from extraintestinal sites and suggest this organism as a possible cause of urinary tract infection.