Description of Comamonas aquatica comb. nov. and Comamonas kerstersii sp. nov. for two subgroups of Comamonas terrigena and emended description of Comamonas terrigena

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 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).

Bacteremia caused by Comamonas kerstersii in a patient with acute perforated appendicitis and localized peritonitis: case report and literature review

Comamonas kerstersii (C. kerstersii) is a Gram-negative bacterium that was initially thought to be non-pathogenic to humans and is abundant in the environment. In recent years, with the availability of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) that enable fast and accurate bacterial identification, there have been increasing number of reports of human infections caused by C. kerstersii, indicating that this organism has emerged as human pathogen. In fact, most clinical isolates of C. kerstersii are recovered from peritoneal liquid, and bacteremia has been infrequently reported. Here, we report a case of bacteremia caused by C. kerstersii in a 28-year-old male patient with acute perforated appendicitis and localized peritonitis and present a comprehensive review of C. kerstersii infections in pathogenic diagnosis and clinical treatment as well as prognosis, thus providing a better understanding of C. kerstersii-related infections.

The Emergence of the Genus Comamonas as Important Opportunistic Pathogens

Comamonas spp. are non-fermenting Gram-negative bacilli. They were first discovered in 1894, and since then, twenty-four species have been characterized. The natural habitat of these bacteria is soil, wastewater/sludge, fresh water such as ponds and rivers, and the animal intestinal microbiome. They were also isolated from industrial settings, such as activated sludge and polluted soil, and from the hospital environment and clinical samples, such as urine, pus, blood, feces, and kidney. Comamonas spp. are associated with environmental bioremediation and are considered an important environmental bacterium rather than a human pathogen. However, in the 1980s, they became a concern when several human infections associated with these species were reported. Here, the Comamonas genus was examined in terms of its members, identification techniques, and pathogenicity. Seventy-seven infection cases associated with these microorganisms that have been discussed in the literature were identified and investigated in this project. All relevant information regarding year of infection, country of origin, patient information such as age, sex, underlying medical conditions if any, type of infection caused by the Comamonas species, antibiotic susceptibility testing, treatment, and outcomes for the patient were extracted from case reports. The findings suggest that even though Comamonas spp. are thought of as being of low virulence, they have caused harmful health conditions in many healthy individuals and even death in patients with underlying conditions. Antimicrobial treatment of infections associated with these species, in general, was not very difficult; however, it can become an issue in the future because some strains are already resistant to different classes of antibiotics. Therefore, these pathogens should be considered of such importance that they should be included in the hospital screening programs.

Maternal peripartum bacteremia caused by intrauterine infection with Comamonas kerstersii: A case report

BACKGROUND

Comamonas kerstersii (C. kerstersii) infections have considered as non-pathogenic to humans, however due to new techniques such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), more cases have been identified.

CASE SUMMARY

This is the first report of a maternal patient with a C. kerstersii bacteremia following caesarean section. Due to the severity of the patient’s condition; high fever and rapidly progressing organ damage, the patient was transferred to the intensive care unit. C. kerstersii was detected by metagenomic next-generation sequencing testing. Based on the drug sensitivity test, appropriate antibiotic treatment was given and the patient recovered fully.

CONCLUSION

This case report confirms that the detection via MALDI-TOF-MS and metagenomic next-generation sequencing testing provides a reliable basis for the diagnosis of this rare bacterial infection.

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 bla_GES-5, bla_OXA, and aminoglycoside resistance (aadA) genes located on putative genomic islands (GIs). All bla_GES-5- and bla_OXA-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 bla_GES-5 or extended-spectrum β-lactamase bla_OXA 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.

Comamonas kerstersii Bacteremia of Unknown Origin

Comamonas kerstersii (C. kerstersii) is a Gram-negative bacillus abundant in the environment and rarely implicated in human disease. Previously considered nonpathogenic, its scarcity in literature may be partly due to the unreliability of past phenotypic tests used for its identification. In recent years, the development of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has enabled fast and accurate laboratory identification of C. kerstersii. Since the first report of human infection in 2013, several others have emerged, with most cases involving peritoneal infection. Here, we present a rare case of C. kerstersii bacteremia in an 82-year-old male patient. With no clear predisposing conditions, the source of his infection is unclear. We accompany this report with a review of C. kerstersii bacteremia cases found in the literature.

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

A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34^T, was isolated from Han River water in the Republic of Korea. Strain CJ34^T 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 CJ34^T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996^T and Comamonas thiooxydans DSM 17888^T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34^T and two closely related type strains C. testosteroni ATCC 11996^T and C. thiooxydans DSM 17888^T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34^T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34^T were C_16 : 0, C_16 : 1  ω6c and/or C_16 : 1  ω7c and C_18 : 1  ω6c and/or C_18 : 1  ω7c. The predominant polar lipids of strain CJ34^T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34^T 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 CJ34^T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34^T (=KACC 22237^T=JCM 34454^T).

Effect of the Manufacturing Process on the Microbiota, Organoleptic Properties and Volatilome of Three Salmon-Based Products

Lightly preserved seafood products, such as cold-smoked fish and fish gravlax, are traditionally consumed in Europe and are of considerable economic importance. This work aimed to compare three products that were obtained from the same batch of fish: cold-smoked salmon (CSS) stored under vacuum packaging (VP) or a modified atmosphere packaging (MAP) and VP salmon dill gravlax (SG). Classical microbiological analyses and 16S rRNA metabarcoding, biochemical analyses (trimethylamine, total volatile basic nitrogen (TVBN), biogenic amines, pH, volatile organic compounds (VOCs)) and sensory analyses (quantitative descriptive analysis) were performed on each product throughout their storage at a chilled temperature. The three products shared the same initial microbiota, which were mainly dominated by Photobacterium, Lactococcus and Lactobacillus genera. On day 28, the VP CSS ecosystem was mainly composed of Photobacterium and, to a lesser extent, Lactococcus and Lactobacillus genera, while Lactobacillus was dominant in the MAP CSS. The diversity was higher in the SG, which was mainly dominated by Enterobacteriaceae, Photobacterium, Lactobacillus and Lactococcus. Although the sensory spoilage was generally weak, gravlax was the most perishable product (slight increase in amine and acidic off-odors and flavors, fatty appearance, slight discoloration and drop in firmness), followed by the VP CSS, while the MAP CSS did not spoil. Spoilage was associated with an increase in the TVBN, biogenic amines and spoilage associated VOCs, such as decanal, nonanal, hexadecanal, benzaldehyde, benzeneacetaldehyde, ethanol, 3-methyl-1-butanol, 2,3-butanediol, 1-octen-3-ol, 2-butanone and 1-octen-3-one. This study showed that the processing and packaging conditions both had an effect on the microbial composition and the quality of the final product.

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

A novel bacterial strain, EJ-4^T, 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-4^T 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 (C_16 : 1  ω7c and/or C_16 : 1  ω6c; 39.7 %) and C_16 : 0 (32.0 %). The G+C content of strain EJ-4^T was 58.4mol %. The average nucleotide identity and digital DNA-DNA hybridization values between strain EJ-4^T 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-4^T, we describe a novel species of the genus Comamonas, for which the name Comamonas suwonensis sp. nov. has been proposed, with EJ-4^T (=KCTC 82074^T=JCM 34179^T=KEMB 1602-279^T) as the type strain.

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.

Exopolysaccharides From Lactobacillus paracasei Isolated From Kefir as Potential Bioactive Compounds for Microbiota Modulation

Microbiota coexists in true symbiosis with the host playing pivotal roles as a key element for well-being and health. Exopolysaccharides from lactic acid bacteria are an alternative as novel potential prebiotics that increase microbiota diversity. Considering this, the aim of the present work was to evaluate the capacity of the EPS produced by two L. paracasei strains isolated from kefir grains, to be metabolized in vitro by fecal microbiota producing short chain fatty acids. For this purpose, fecal samples from healthy children were inoculated in a basal medium with EPS and incubated in anaerobiosis at 37°C for 24, 48, and 72 h. DGGE profiles and the production of SCFA after fermentation were analyzed. Additionally, three selected samples were sequenced by mass sequencing analysis using Ion Torrent PGM. EPS produced by L. paracasei CIDCA 8339 (EPS₈₃₃₉) and CIDCA 83124 (EPS₈₃₁₂₄) are metabolized by fecal microbiota producing a significant increase in SCFA. EPS₈₃₃₉ fermentation led to an increment of propionate and butyrate, while fermentation of EPS₈₃₁₂₄ increased butyrate levels. Both EPS led to a profile of SCFA different from the ones obtained with inulin or glucose fermentation. DGGE profiles of 72 h fermentation demonstrated that both EPS showed a different band profile when compared to the controls; EPS profiles grouped in a cluster that have only 65% similarity with glucose or inulin profiles. Mass sequencing analysis demonstrated that the fermentation of EPS₈₃₃₉ leads to an increase in the proportion of the genera Victivallis, Acidaminococcus and Comamonas and a significant drop in the proportion of enterobacteria. In the same direction, the fermentation of EPS₈₃₁₂₄ also resulted in a marked reduction of Enterobacteriaceae with a significant increase in the genus Comamonas. It was observed that the changes in fecal microbiota and SCFA profile exerted by both polymers are different probably due to differences in their structural characteristics. It can be concluded that EPS synthesized by both L. paracasei strains, could be potentially used as bioactive compound that modify the microbiota increasing the production of propionic and butyric acid, two metabolites highly associated with beneficial effects both at the gastrointestinal and extra-intestinal level.

The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence

Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of Comamonas have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of Comamonas to different environments as well as the virulence of potentially pathogenic Comamonas strains. In this study, we provide genomic insights into the potential ecological roles and virulence of Comamonas by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different Comamonas species. The analyses revealed that the metabolic pathways enabling Comamonas to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in Comamonas, suggesting that Comamonas plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in Comamonas were found to be highly species-specific. The conserved strategies used by potentially pathogenic Comamonas for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.

Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis

Because of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-time (SMRT) analysis. Protein-coding genes, rRNAs and tRNAs were predicted. Functional annotations of the genome using different databases revealed several genes related to pathogenicity including antibiotic resistance genes and prophages. Our work demonstrates that whole genome sequencing can enhance the resolution of clinical investigations and our data can be used as a reference genome during the rapid diagnosis of C. kerstersii infections in the future.

First report of Comamonas kerstersii causing urinary tract infection

The association of Comamonas kerstersii with peritonitis resulting from perforated appendix and its isolation from a psoas abscess and pelvic peritonitis have previously been described by us. We present the first case of C. kerstersii urinary tract infection, broadening the spectrum of infections caused by this species.

Comamonas kerstersii bacteremia in a patient with acute perforated appendicitis: A rare case report

RATIONALE

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, C. kerstersii maybe be confused with Comamonas testosteroni using the automatic bacterial identification systems currently available.

PATIENT CONCERNS

A 31-year-old man who had onset of left upper abdominal pain developed clinical manifestations of right lower abdominal pain and classic migration of pain at the temperature of 39°C. The positive strain of aerobic and anaerobic bottles of blood cultures was identified.

DIAGNOSES

The patient was diagnosed as acute peritonitis and perforated appendix with abdominal abscess.

INTERVENTIONS

The bacterium was identified by routine methods, MALDI-TOF-MS and PCR amplification of the 16S rRNA. The patient was treated with exploratory laparotomy, appendectomy, tube drainage, and prescribing antibiotic treatment.

OUTCOMES

The patients were discharged with complete recovery. The organisms were confirmed as C. kerstersii by MALDI-TOF-MS and a combination of the other results.

LESSONS

Our findings suggest that C. kerstersii infection occurs most often in association with perforated appendix and bacteremia. We presume that C. kerstersii is an opportunistic pathogen or commensal with the digestive tract and appendix bacteria.

Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh

Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.IMPORTANCE The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.

Unusual presentations of Comamonas kerstersii infection

The association of Comamonas kerstersii with peritonitis resulting from the presence of perforated appendix has previously been described by our research team. In the present study, we describe the isolation of this microorganism from two forms of unusual presentations of C. kerstersii infection not previously described in the literature: localized intra-abdominal infection (psoas abscess) and pelvic peritonitis.

Draft Genome Sequence of the Bacterium Comamonas aquatica CJG

A Gram-negative bacterial strain, Comamonas aquatica CJG, absorbs low-density lipoprotein but not high-density lipoprotein in serum. Here, we report its draft genomic sequence of 3,764,434 bp, containing total 3,425 genes, 27% of which encode proteins for metabolism and energy conversion, and it is 30% identical to the genome of Comamonas testosteroni.

High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

BACKGROUND

Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to multiple heavy metals and multiple drugs. However, comprehensive genomic analysis among the C. testosteroni strains is lacked.

RESULTS

To understand the genome bases of the features of C. testosteroni, we sequenced 10 strains of this species and analyzed them together with other related published genome sequences. The results revealed that: 1) the strains of C. testosteroni have genome sizes ranging from 5.1 to 6.0 Mb and G + C contents ranging from 61.1% to 61.8%. The pan-genome contained 10,165 gene families and the core genome contained 3,599 gene families. Heap's law analysis indicated that the pan-genome of C. testosteroni may be open (α = 0.639); 2) by analyzing 31 phenotypes of 11 available C. testosteroni strains, 99.4% of the genotypes (putative genes) were found to be correlated to the phenotypes, indicating a high correlation between phenotypes and genotypes; 3) gene clusters for nitrate reduction, steroids degradation and metal and multi-drug resistance were found and were highly conserved among all the genomes of this species; 4) the genome similarity of C. testosteroni may be related to the geographical distances.

CONCLUSIONS

This work provided an overview on the genomes of C. testosteroni and new genome resources that would accelerate the further investigations of this species. Importantly, this work focused on the analysis of potential genetic determinants for the typical characters and found high correlation between the phenotypes and their corresponding genotypes.

Comamonas humi sp. nov., isolated from soil

A bacterial strain, designated GAU11T, was isolated from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic, non-motile rods. The 16S rRNA gene sequence of strain GAU11T showed high similarity to those of Comamonas zonglianii BF-3T (98.8 %), Pseudacidovorax intermedius CC21T (96.4 %), Acidovorax caeni R-24608T (96.2 %), Alicycliphilus denitrificans K601T (96.2 %), Pseudorhodoferax soli TBEA3T (95.9 %) and Comamonas terrigena LMG 1253T (95.9 %). Strain GAU11T contained ubiquinone 8 as the sole ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Its major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain GAU11T was 68.2 mol%. The DNA–DNA relatedness between strain GAU11T and C. zonglianii DSM 22523T was 52 or 68 % (reciprocal value). Phenotypic characterization indicated that strain GAU11T represents a member of the genus Comamonas , but at the same time distinguished it from C. zonglianii DSM 22523T. From polyphasic characterization, this strain should be classified as representing a novel species of the genus Comamonas , for which the name Comamonas humi sp. nov. (type strain GAU11T = JCM 19903T = DSM 28451T) is proposed.

Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms

The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.

Characterization of SDS-degrading Delftia acidovorans and in situ monitoring of its temporal succession in SDS-contaminated surface waters

Incomplete removal of sodium dodecyl sulfate (SDS) in wastewater treatment plants may result in SDS residues escaping and finding their way into receiving water bodies like rivers, lakes, and sea. Introduction of effective microorganisms into the aerobic treatment facilities can reduce unpleasant by-products and SDS residues. Selecting effective microorganisms for SDS treatment is a big challenge. Current study reports the isolation, identification, and in situ monitoring of an effective SDS-degrading isolate from detergent-polluted river waters. Screening was carried out by the conventional enrichment culture technique and the isolate was tentatively identified by using fatty acid methyl ester and 16S ribosomal RNA (rRNA) sequence analyses. Fatty acids produced by the isolate investigated were assumed as typical for the genus Comamonas. 16S rRNA sequence analysis also confirmed that the isolate had 95% homology with Delftia acidovorans known as Comamonas or Pseudomonas acidovorans previously. D. acidovorans exhibited optimum growth at SDS concentration of 1 g l(-1) but tolerated up to 10 g l(-1) SDS. 87% of 1.0 g l(-1) pure SDS was degraded after 11 days of incubation. The temporal succession of D. acidovorans in detergent-polluted river water was also monitored in situ by using Comamonas-specific fluorescein-labeled Cte probe. Being able to degrade SDS and populate in SDS-polluted surface waters, D. acidovorans isolates seem to be very helpful in elimination of SDS.

Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits

Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development, and reduces fertility but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid, preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology.

Bacteremia caused by Comamonas kerstersii in a patient with diverticulosis

We report for the first time a case of bacteremia caused by Comamonas kerstersii in a 65-year-old patient with sign of diverticulosis. In addition, we review the isolation of Comamonas sp. and related organisms in our hospital over 25 years.

Comamonas jiangduensis sp. nov., a biosurfactant-producing bacterium isolated from agricultural soil

A novel biosurfactant-producing strain, designated YW1T, was isolated from agricultural soil. Its taxonomic position was investigated using a polyphasic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YW1T was a member of the genus Comamonas , and showed highest sequence similarities to Comamonas aquatica LMG 2370T (98.5 %), Comamonas kerstersii LMG 3475T (97.7 %) and Comamonas terrigena LMG 1253T (97.7 %). Furthermore, DNA–DNA hybridization experiments against these three strains gave results that were clearly lower than 70 % DNA–DNA similarity, and consequently confirmed that this new strain does not belong to a previously described species of the genus Comamonas . The major respiratory quinone was ubiquinone-8. The major fatty acids (>5 %) were C16 : 0 (30.1 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 25.4 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c; 15.3 %), C17 : 0 cyclo (7.4 %) and C14 : 0 (5.8 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipids and unknown lipids. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain YW1T was clearly distinguishable from all species of the genus Comamonas with validly published names and should be classified as a representative of a novel species of the genus Comamonas , for which the name Comamonas jiangduensis sp. nov. is proposed. The type strain is YW1T ( = CCTCC AB 2012033T = KACC 16697T).

Intra-abdominal infections due to Comamonas kerstersii

Herein, we report four cases of Comamonas kerstersii intra-abdominal infections representing the first report of human infections caused by this Comamonas species. In addition, our work demonstrates the association of C. kerstersii with peritonitis secondary to appendix rupture.

Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae

A novel strain, named S4(T), was obtained from industrial wastewater in Xiaoshan, Zhejiang Province, China. Cells were Gram-negative, neutrophilic and non-spore-forming and moved by means of a polar flagellum. Normal cells were 0.8-0.9 × 1.3-1.9 µm and the cells elongated to 10-25 µm when cultivated at high temperatures. Strain S4(T) grew at 15-50 °C (optimum at 48 °C), pH 5.5-8.5 (optimum 7.0-7.5) and 0-2% (optimum 0.5%) (w/v) NaCl. Ubiquinone-8 was the predominant respiratory quinone. C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and C17:0 cyclo were the major cellular fatty acids. The major 3-OH fatty acid was C10:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminoglycolipid. The genomic DNA G+C content was 68.8 mol%. Based on 16S rRNA gene sequences alignment, the most closely related strains were members of the genera Comamonas (94.6-95.6% similarities), Giesbergeria (94.9-95.6%), Acidovorax (94.8-95.4%), Brachymonas (94.1-95.2%) and Macromonas (95.1%). Phylogenetic analysis showed the closest relatives of strain S4(T) were members of the genus Macromonas. Based on phenotypic and phylogenetic characteristics, we suggest that strain S4(T) represents a novel species of a new genus of the family Comamonadaceae, for which the name Extensimonas vulgaris gen. nov., sp. nov. is proposed. The type strain of Extensimonas vulgaris is S4(T) (=CGMCC 1.10977(T)=JCM 17803(T)).

Microbial diversity in anaerobic sediments at Rio Tinto, a naturally acidic environment with a high heavy metal content

The Tinto River is an extreme environment located at the core of the Iberian Pyritic Belt (IPB). It is an unusual ecosystem due to its size (100 km long), constant acidic pH (mean pH, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the Tinto River Basin comparable to acidic mine drainage (AMD) systems. In this paper we present an extensive survey of the Tinto River sediment microbiota using two culture-independent approaches: denaturing gradient gel electrophoresis and cloning of 16S rRNA genes. The taxonomic affiliation of the Bacteria showed a high degree of biodiversity, falling into 5 different phyla: Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria; meanwhile, all the Archaea were affiliated with the order Thermoplasmatales. Microorganisms involved in the iron (Acidithiobacillus ferrooxidans, Sulfobacillus spp., Ferroplasma spp., etc.), sulfur (Desulfurella spp., Desulfosporosinus spp., Thermodesulfobium spp., etc.), and carbon (Acidiphilium spp., Bacillus spp., Clostridium spp., Acidobacterium spp., etc.) cycles were identified, and their distribution was correlated with physicochemical parameters of the sediments. Ferric iron was the main electron acceptor for the oxidation of organic matter in the most acid and oxidizing layers, so acidophilic facultative Fe(III)-reducing bacteria appeared widely in the clone libraries. With increasing pH, the solubility of iron decreases and sulfate-reducing bacteria become dominant, with the ecological role of methanogens being insignificant. Considering the identified microorganisms-which, according to the rarefaction curves and Good's coverage values, cover almost all of the diversity-and their corresponding metabolism, we suggest a model of the iron, sulfur, and organic matter cycles in AMD-related sediments.

Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil

A bacterial strain, designated BF-3T, was isolated from phenol-contaminated soil and investigated using a polyphasic taxonomic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BF-3T formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Comamonas; it showed highest sequence similarities to Comamonas aquatica LMG 2370T (96.8 %), C. nitrativorans DSM 13191T (96.4 %), C. odontotermitis LMG 23579T (96.4 %), C. kerstersii LMG 3475T (96.3 %), C. koreensis KCTC 12005T (96.1 %) and C. terrigena LMG 1253T (96.0 %). The major cellular fatty acids were C16 : 0, C18 : 1/C18 : 1 ω7c, C17 : 0 cyclo and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain BF-3T was clearly distinct from type strains of other recognized species of the genus Comamonas and, as such, represents a novel species of the genus Comamonas, for which the name Comamonas zonglianii sp. nov. is proposed. The type strain is BF-3T (=CCTCC AB 209170T =DSM 22523T).

Bacterial community dynamics during the application of a Myxococcus xanthus-inoculated culture medium used for consolidation of ornamental limestone

In this study, we investigated under laboratory conditions the bacterial communities inhabiting quarry and decayed ornamental carbonate stones before and after the application of a Myxococcus xanthus-inoculated culture medium used for consolidation of the stones. The dynamics of the community structure and the prevalence of the inoculated bacterium, M. xanthus, were monitored during the time course of the consolidation treatment (30 days). For this purpose, we selected a molecular strategy combining fingerprinting by denaturing gradient gel electrophoresis (DGGE) with the screening of eubacterial 16S rDNA clone libraries by DGGE and sequencing. Quantification of the inoculated strain was performed by quantitative real-time PCR (qPCR) using M. xanthus-specific primers designed in this work. Results derived from DGGE and sequencing analysis showed that, irrespective of the origin of the stone,the same carbonatogenic microorganisms were activated by the application of a M. xanthus culture. Those microorganisms were Pseudomonas sp., Bacillus sp., and Brevibacillus sp. The monitoring of M. xanthus in the culture media of treated stones during the time course experiment showed disparate results depending on the applied technique. By culture-dependent methods, the detection of this bacterium was only possible in the first day of the treatment, showing the limitation of these conventional techniques. By PCR-DGGE analysis, M. xanthus was detected during the first 3-6 days of the experiment. At this time, the population of this bacterium in the culture media varied between 108-106 cells ml-1, as showed by qPCR analyses. Thereafter, DGGE analyses showed to be not suitable for the detection of M. xanthus in a mixed culture. Nevertheless, qPCR analysis using specific primers for M. xanthus showed to bea more sensitive technique for the detection of thisbacterium, revealing a population of 104 cells ml-1 in the culture media of both treated stones at the end of the consolidation treatment. The molecular strategy used in this study is proposed as an effective monitoring system to evaluate the impact of the application of a bacterially induced carbonate mineralization as restoration/conservation treatment for ornamental stones.

Reclassification of Aquaspirillum itersonii and Aquaspirillum peregrinum as Novispirillum itersonii gen. nov., comb. nov. and Insolitispirillum peregrinum gen. nov., comb. nov

Phylogenetic analysis based on 16S rRNA gene sequences showed that Aquaspirillum itersonii and Aquaspirillum peregrinum form distinct phylogenetic lineages within the Alphaproteobacteria, whereas Aquaspirillum serpens, the type species of the genus Aquaspirillum, belongs to the Betaproteobacteria. A. itersonii and A. peregrinum exhibited 16S rRNA gene sequence similarity values of 82.0-82.4 % to the type strain of A. serpens and of 91.8-92.0 % to each other. A. itersonii and A. peregrinum were clearly distinguishable from A. serpens by differences in ubiquinone types and fatty acid profiles. A. itersonii subsp. itersonii LMG 4337(T) and A. itersonii subsp. nipponicum LMG 7370(T) contained Q-10 as the predominant ubiquinone, and A. peregrinum subsp. peregrinum LMG 4340(T) and A. peregrinum subsp. integrum LMG 5407(T) contained Q-9 as the predominant ubiquinone, whereas A. serpens LMG 3734(T) had Q-8 as the predominant ubiquinone. A. itersonii and A. peregrinum were also distinguishable from A. serpens by some differences in the fatty acid composition, including major fatty acids and hydroxy fatty acids. On the basis of these data, A. itersonii and A. peregrinum should be reclassified into two novel genera and species, for which the names Novispirillum itersonii gen. nov., comb. nov. and Insolitispirillum peregrinum gen. nov., comb. nov., respectively, are proposed.

Phylogenetic and functional diversity of bacteria in biofilms from metal surfaces of an alkaline district heating system

District heating systems (DHS) are extreme aqueous environments characterized by high temperatures, high pH (9.5-10.0), and low nutrient availability. Culture-independent and culture-dependent techniques showed that DHS may nevertheless harbour geno- and phenotypically diverse bacterial biofilm communities. Approximately 50% of the cells in biofilms growing on mild steel coupons in rotortorque reactors connected to the return line (40 degrees C) of a Danish DHS were detectable by FISH analysis and thus were probably metabolically active. A bacterial 16S rRNA gene clone library generated from the biofilms was dominated by proteobacterial phylotypes (closely related to known aerobic species) and by phylotypes affiliated to the anaerobic class Clostridia. Anoxic enrichment cultures derived from biofilms primarily contained 16S rRNA gene and dsrAB (encoding major subunits of dissimilatory sulfite reductase) phylotypes affiliated to the latter class. Alkalitolerant and neutrophilic anaerobic bacteria were isolated from the DHS, including novel Gram-positive and deltaproteobacterial sulfate-reducers and sulfite-reducers constituting novel Gram-positive lineages. In total, 39 distinct 16S rRNA gene phylotypes representing ten classes were identified. The detection of several alkalitolerant, sulfide-producing, and, thus, potentially biocorrosive species underlines the need to maintain a high water quality in the DHS in order to prevent the proliferation of these species.

Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus

A bacterial strain, designated Dant 3-8T, isolated from the gut of the termite Odontotermes formosanus, was investigated by a polyphasic taxonomic approach. The cells were rod-shaped, Gram-negative, non-pigmented, non-spore-forming and non-fermentative. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbours being Comamonas testosteroni DSM 50244T (96.4 % sequence similarity), Comamonas koreensis KCTC 12005T (96.0 %) and Comamonas terrigena DSM 7099T (96.2 %). Strain Dant 3-8T was clearly distinguished from all of these strains by using phylogenetic analysis, DNA–DNA hybridization, whole-cell protein profiles, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that Dant 3-8T represents a novel species in the genus Comamonas, for which the name Comamonas odontotermitis sp. nov. is proposed. The type strain is Dant 3-8T (=BCRC 17576T=LMG 23579T).

Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient

To determine whether the distribution of estuarine ammonia-oxidizing bacteria (AOB) was influenced by salinity, the community structure of betaproteobacterial ammonia oxidizers (AOB) was characterized along a salinity gradient in sediments of the Ythan estuary, on the east coast of Scotland, UK, by denaturant gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rRNA gene fragments. Ammonia-oxidizing bacteria communities at sampling sites with strongest marine influence were dominated by Nitrosospira cluster 1-like sequences and those with strongest freshwater influence were dominated by Nitrosomonas oligotropha-like sequences. Nitrosomonas sp. Nm143 was the prevailing sequence type in communities at intermediate brackish sites. Diversity indices of AOB communities were similar at marine- and freshwater-influenced sites and did not indicate lower species diversity at intermediate brackish sites. The presence of sequences highly similar to the halophilic Nitrosomonas marina and the freshwater strain Nitrosomonas oligotropha at identical sampling sites indicates that AOB communities in the estuary are adapted to a range of salinities, while individual strains may be active at different salinities. Ammonia-oxidizing bacteria communities that were dominated by Nitrosospira cluster 1 sequence types, for which no cultured representative exists, were subjected to stable isotope probing (SIP) with 13C-HCO3-, to label the nucleic acids of active autotrophic nitrifiers. Analysis of 13C-associated 16S rRNA gene fragments, following CsCl density centrifugation, by cloning and DGGE indicated sequences highly similar to the AOB Nitrosomonas sp. Nm143 and Nitrosomonas cryotolerans and to the nitrite oxidizer Nitrospira marina. No sequence with similarity to the Nitrosospira cluster 1 clade was recovered during SIP analysis. The potential role of Nitrosospira cluster 1 in autotrophic ammonia oxidation therefore remains uncertain.

Comamonas badia sp. nov., a floe-forming bacterium isolated from activated sludge

Strain IAM 14839, isolated from activated sludge in Japan, forms a visible floc and grows in the flocculated state. This bacterium is Gram-negative, rod-shaped, strictly aerobic and highly motile with a single polar flagellum. Both oxidase and catalase activities are positive. No growth was observed on sugars. The strain can grow at 20 degrees C, but does not grow at 37 degrees C. The G+C content of DNA is 66.3 mol% and Q-8 is the major quinone. The major cellular fatty acids are 16:1omega7c, 16:0, 18:1omega7c, 2OH 16:0, 3OH 10:0. The 16S rDNA sequence analysis indicated that the bacterium clustered within the genus Comamonas. On the basis of the phylogenetic analysis and phenotypic properties, it is proposed that the strain IAM 14839T be classified in a novel species of the genus Comamonas, Comamonas badia sp. nov. The type strain is IAM 14839T (=KCTC 12244T ).