Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine

Controlled Substance Liquid Waste Management Systems As Potential Reservoirs for Nosocomial Infection in a Pediatric Hospital

OBJECTIVE

The purpose of this study was to determine if controlled substance waste management systems (CSWMS) demonstrate microbial growth, and therefore present a potential infection risk to pediatric hospital patients.

METHODS

Twenty CSWMS, either Smart Sink or Pharma Lock systems, located in patient care areas were sampled. Twelve were located in critical care areas. Cultures were obtained by swabbing the drain grate with a sterile swab. Swabs were then transported to the microbiology lab for culture. Each sample was labeled with the location of the CSWMS and each system was photographed.

RESULTS

Of the CSWMS sampled, 50% demonstrated bacterial or fungal growth with a total of 15 microorganisms isolated, including 3 systems with Micrococcus luteus, 2 with Aspergillus species, and 2 with -Bacillus cereus. Nine of the 15 microorganisms isolated were from systems in the pediatric intensive care unit (PICU) followed by 2 microorganisms in the neonatal intensive care unit (NICU). Of the 12 systems sampled in critical care areas, 8 (66%) had positive cultures. Of the 10 systems which demonstrated growth, 9 were Pharma Lock and 1 was Smart Sink.

CONCLUSION

Controlled substance waste management systems harbor potential pathogens and may serve as reservoirs of infectious agents in pediatric hospitals. Microbial growth was identified in more than half of sampled CSWMS located in critical care areas, where the most vulnerable patients are located. Based on this study, a cleaning procedure for CSWMS should be implemented. Further investigation on the relationship between CSWMS and nosocomial infections is warranted.

Uncommon Septic Arthritis of the Hip Joint in an Immunocompetent Adult Patient Due to Bacillus pumilus and Paenibacillus barengoltzii Managed with Long-Term Treatment with Linezolid: A Case Report and Short Literature Review

The Bacillus and Paenibacillus genera are diverse soil-related bacterial pathogens. In this case report, we describe, to our knowledge, the first report of septic arthritis in a native hip joint in an immunocompetent adult patient caused by Bacillus pumilus and Paenibacillus barengoltzii. We describe the case of a 39-year-old Caucasian male patient who sought medical advice for chronic pain on the mobilization of the right hip, decreased range of motion, and physical asthenia. The patient underwent a surgical intervention (core decompression) for a right osteonecrosis of the femoral head, with a slightly favorable postoperative evolution after surgery for one month. Surgical treatment was planned on the basis of clinical and paraclinical investigations and the joint damage. The hip was explored using an anterior approach under spinal anesthesia and standard antibiotic prophylaxis. After resection of the femoral head, meticulous debridement of all inflammatory tissues was performed, and a preformed temporary spacer was inserted into the femoral canal. Bacteriological laboratory studies identified Bacillus pumilus and Paenibacillus barengoltzii via matrix-assisted laser desorption-ionization time-of-flight mass spectrometry analysis. The patient initially received nine days of empirical therapy with intravenous antibiotics (linezolid and meropenem). After the bacterial strains were identified, the patient received organism-specific antibiotic therapy with the same antibiotics and dose for eight days until discharge. After discharge, the patient was referred to another hospital, where he continued treatment with linezolid for seven weeks and, after that, four weeks of oral therapy with cotrimoxazole and rifampicin. During this period, no severe or potentially life-threatening adverse events were recorded during long-term treatment with linezolid or with the two oral antibiotics. In conclusion, our findings suggest that long-term treatment with linezolid may be a viable option for the management of bone and joint infections caused by Bacillus pumilus and Paenibacillus barengoltzii.

Paenibacillus polygoni sp. nov., an endophytic bacterium isolated from Polygonum lapathifolium L. in wetland

A Gram-stain-positive, aerobic, rod-shaped, non-motile, yellowish and glossy strain, C31T, was isolated from a wetland plant Polygonum lapathifolium L. located south of Poyang Lake, Jiangxi Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C31T showed similarity values of lower than 97.0 % to other type species belonging to the genus Paenibacillus. The genomic average nucleotide identity values between strain C31T and its reference type species ranged from 68.9-70.9 % and the digital DNA-DNA hybridization values were lower than 27.8 %. The genomic DNA G+C content of strain C31T was 41.9 mol%. The optimal growth temperature, pH and NaCl concentration were 37 °C, pH 7 and 0.5 %, respectively. The major cellular fatty acids (>5.0 %) of strain C31T were anteiso-C15 : 0 (73.7 %), anteiso-C17 : 0 (8.4 %) and iso-C15 : 0 (5.2 %). The polar lipids of strain C31T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The respiratory quinone was MK-7. Based on these phylogenetic and phenotypic characterizations, strain C31T represents a novel species within the genus Paenibacillus. Therefore, the proposed name for this newly identified species is Paenibacillus polygoni sp. nov. and the type strain is C31T (=CCTCC AB 2022349T=KCTC 43565T).

Human Paenibacillus Infections: A Systematic Review with Comparison of Adult and Infant Cases

Neonatal infections due to Paenibacillus species have increasingly been reported over the last few years. We performed a structured literature review of human Paenibacillus infections in infants and adults to compare the epidemiology of infections between these distinct patient populations. Thirty-nine reports describing 176 infections met our inclusion criteria and were included. There were 37 Paenibacillus infections occurring in adults caused by 23 species. The clinical presentations of infections were quite variable. In contrast, infections in infants were caused by only 3 species: P. thiaminolyticus (112/139, 80%), P. alvei (2/139, 1%) and P. dendritiformis (2/139, 1%). All of the infants with Paenibacillus infection presented with a sepsis syndrome or meningitis, often complicated by extensive cerebral destruction and hydrocephalus. Outcomes were commonly poor with 17% (24/139) mortality. Cystic encephalomalacia due to brain destruction was common in both Ugandan and American cases and 92/139 (66%) required surgical management of hydrocephalus following their infection. Paenibacillus infections are likely underappreciated in infants and effective treatments are urgently needed.

The transmittable through stinging microbiota differs between honeybees and wasps: a potentially greater microbial risk of the wasp sting for humans

The present research investigated whether accidental contact through stinging with honeybees, wasps, and hornets could represent a microbial hazard for humans. It has been previously suggested that such contact may transmit pathogens causing infections that could even be fatal for some susceptible individuals. Stinging simulation experiments were performed in the lab with live insects collected from the environment in Lemnos Island (north-eastern Greece), while different selective agar media targeting some clinically important bacteria (i.e., Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis/faecium, and Pseudomonas aeruginosa) were used as substrates for microbial recovery and identification. Results revealed none of the target pathogenic bacterial species in the honeybee samples, with bacilli, staphylococci, and micrococci dominating their surveyed microbiota. However, most of the suspect colonies isolated from wasps and hornets belonged to important hygienic indicators (i.e., enterococci, Proteus mirabilis, and coliforms), implying possible contact of these insects with fecal origin materials. To sum up, the microbiota that may be transmitted to humans through stinging appears to differ between honeybees and wasps/hornets, while the isolation from the latter samples of some other important opportunistic pathogens, such as Enterobacter spp. and Klebsiella spp., also known for multidrug resistance, could be an additional reason of concern.

Paenibacillus amylolyticus osteomyelitis in a Poodle dog: case report and literature review

Paenibacilli are gram-variable, endospore-forming bacteria that occupy various ecologic niches. These microorganisms have been known to infect humans occasionally at various anatomic sites. However, in humans, as well as in other vertebrate animals, the relationship between disease and isolation of Paenibacillus spp. remains poorly understood. We report here a case of infection in an adult Poodle dog. The animal had nodules in the lungs and multifocal osteolytic expansile bone lesions. From bone, Paenibacillus amylolyticus was recovered by culture and identified by MALDI-TOF mass spectroscopy and 16S rDNA sequencing; pyogranulomatous inflammation was observed in lung and bone specimens. The microorganism was resistant to clindamycin and imipenem. Four-month treatment with amoxicillin–clavulanate resulted in clinical resolution of disease in this dog. Nevertheless, therapy for more prolonged periods should be considered because recurrent infections can occur as a result of the transition of Paenibacillus spores to vegetative cells. Disease caused by a Paenibacillus species has not been reported previously in dogs, to our knowledge.

Design and Experimental Evaluation of a New RNA-FISH Probe to Detect and Identify Paenibacillus sp

Paenibacillus, rod-saped gram-positive endospores forming aerobic or facultative anaerobic bacteria, colonize diverse ecosystems and are involved in the biodegradation of cultural heritage assets. Biodeteriogenic microorganisms can be easily detected/identified by ribonucleic acid- fluorescent in situ hybridization RNA-FISH with specific probes. In this work, probes designed in silico were analyzed to calculate hybridization efficiency and specificity by varying the formamide concentration in the hybridization. The Pab489 probe showed excellent in silico performance with high theoretical maximum efficiency hybridization (99.99%) and specificity and was selected for experimental assays with target Paenibacillus sp. and non-target biodeteriogenic microorganisms. Results assessed by epifluorescence microscopy and flow cytometry revealed that, regardless of the formamide concentration, it was possible to observe that the Pab489-Cy3 probe had a similar signal intensity to the EUB338-Cy3 probe (positive control), so the presence of formamide, a highly toxic and carcinogenic compound used to aid the hybridization process, is not necessary. The designed probe used in FISH assays allows specific in situ identification of Paenibacillus spp. in microbial communities in a culture-independent way. This approach can be employed for screening Paenibacillus spp., showing great potential for future application in biodeterioration of heritage assets, in the search for Paenibacillus strains that produce compounds with biotechnological or medical potential.

Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup

Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2^T and UniB3^T, were isolated from digestive syrup containing fungal diastase (10 mg/ml), pepsin (2 mg/ml) and sugar base containing polyethylene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2^T has the highest sequence similarity with Paenibacillus humicus NBRC 102415^T (98.3%) and strain UniB3^T showed the highest sequence similarity with Niallia circulans DSM 11^T (98.9%). The DNA G + C content of UniB2^T was 63.7 mol %. The dDDH and ANI values between the strain UniB2^T and its phylogenetically close relative were < 38.3% and < 89.5%, respectively. The major fatty acids of the strain UniB2^T were C_16:0 (13.9%), C_15:0 anteiso (39.7%), C_17:0 anteiso (15.5%). The DNA G + C content of UniB3^T was 35.6 mol %. The dDDH and ANI values between the strain UniB3^T and its close relatives were < 29.1% and 84.6%, respectively. The major fatty acids of strain UniB3^T were C_16:0 (13.5%), C_15:0 anteiso (40.1%) and C_17:0 anteiso (16.0%). Major polar lipids for both strains were Diphosphatidylglycerol and phosphatidylethanolamine. Both strains showed unique carbon utilization and assimilation pattern that differentiated them from their phylogenetically related neighbours. These phenotypic, genotypic and chemotaxonomic characters indicated the strains UniB2^T and UniB3^T represent two novel species for which the names Paenibacillus albicereus sp. nov. (Type strain UniB2^T = MCC 3997^T = KCTC 43095^T = JCM34513^T) and Niallia alba sp. nov. (Type strain UniB3^T = MCC 3998^T = KCTC 43235^T = JCM 34492^T) are proposed.

Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants

Postinfectious hydrocephalus (PIH), which often follows neonatal sepsis, is the most common cause of pediatric hydrocephalus worldwide, yet the microbial pathogens underlying this disease remain to be elucidated. Characterization of the microbial agents causing PIH would enable a shift from surgical palliation of cerebrospinal fluid (CSF) accumulation to prevention of the disease. Here, we examined blood and CSF samples collected from 100 consecutive infant cases of PIH and control cases comprising infants with non-postinfectious hydrocephalus in Uganda. Genomic sequencing of samples was undertaken to test for bacterial, fungal, and parasitic DNA; DNA and RNA sequencing was used to identify viruses; and bacterial culture recovery was used to identify potential causative organisms. We found that infection with the bacterium Paenibacillus, together with frequent cytomegalovirus (CMV) coinfection, was associated with PIH in our infant cohort. Assembly of the genome of a facultative anaerobic bacterial isolate recovered from cultures of CSF samples from PIH cases identified a strain of Paenibacillus thiaminolyticus This strain, designated Mbale, was lethal when injected into mice in contrast to the benign reference Paenibacillus strain. These findings show that an unbiased pan-microbial approach enabled characterization of Paenibacillus in CSF samples from PIH cases, and point toward a pathway of more optimal treatment and prevention for PIH and other proximate neonatal infections.

Paenibacillus zeisoli sp. nov., isolated from maize-cultivated soil artificially contaminated with cadmium

A Gram-stain-negative, rod-shaped, motile bacterial strain, designated 3-5-3T, was isolated from maize-cultivated soil artificially contaminated with cadmium, in Nanyang, Henan Province, China. Strain 3-5-3T was oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-5-3T was affiliated with the genus Paenibacillus and most closely related to Paenibacillus anaericanus MH2T (96.5 % similarity). The average nucleotide identity and digital DNA–DNA hybridization values between 3-5-3T and the closely related species ranged 69.4–84.5 % and 18.1–18.4 %. The genomic G+C content was 53.8 mol%. Anteiso-C15 : 0 was the major fatty acid and MK-7 was the only menaquinone. The diamino acid in the cell-wall peptidoglycan contains meso-diaminopimelic acid. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, two unidentified glycolipids, two unidentified aminolipids, one unidentified phospholipid, one unidentified phosphoaminolipid and six unidentified lipids. On the basis of the results obtained in this study, strain 3-5-3T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus zei soli sp. nov. is proposed. The type strain is 3-5-3T (=CGMCC 1.13686T=KCTC 33998T).

Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France

The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.

Tailor-made exopolysaccharides-CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa

Application of state-of-the-art genome editing tools like CRISPR-Cas9 drastically increase the number of undomesticated micro-organisms amenable to highly efficient and rapid genetic engineering. Adaptation of these tools to new bacterial families can open up entirely new possibilities for these organisms to accelerate as biotechnologically relevant microbial factories, also making new products economically competitive. Here, we report the implementation of a CRISPR-Cas9 based vector system in Paenibacillus polymyxa, enabling fast and reliable genome editing in this host. Homology directed repair allows for highly efficient deletions of single genes and large regions as well as insertions. We used the system to investigate the yet undescribed biosynthesis machinery for exopolysaccharide (EPS) production in P. polymyxa DSM 365, enabling assignment of putative roles to several genes involved in EPS biosynthesis. Using this simple gene deletion strategy, we generated EPS variants that differ from the wild-type polymer not only in terms of monomer composition, but also in terms of their rheological behavior. The developed CRISPR-Cas9 mediated engineering approach will significantly contribute to the understanding and utilization of socially and economically relevant Paenibacillus species and extend the polymer portfolio.

Paenibacillus shunpengii sp. nov., isolated from farmland soil

A bacterial strain designated YYJ7-1^T was isolated from farmland soil in China and characterized using a polyphasic taxonomic approach. Cells of strain YYJ7-1^T were Gram-staining-positive, aerobic or facultatively anaerobic, rod-shaped, motile and endospore-forming. Growth occurred at 18-42 °C (optimum at 35 °C), at pH 6.0-8.0 (optimum at pH 7.5) and with 0.0-4.0 % NaCl (optimum with 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Paenibacillus and showed high levels of sequence similarity with respect to Paenibacillus provencensis 4401170^T (98.6 %) and Paenibacillus urinalis 5402403^T (98.4 %), while lower 16S rRNA gene sequence similarities were observed with all other type strains (97.0 %). However, strain YYJ7-1^T showed low DNA-DNA relatedness with P. provencensis 4401170^T 48.7±4.5 % (43.6±7.1 % in a reciprocal experiment), and P. urinalis 5402403^T 38.9±5.7 % (35.6±6.8 %). The major cellular fatty acids (>10.0 %) of strain YYJ7-1^T were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipid profile consisted of phospholipids, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major isoprenoid quinone was MK-7. The DNA G+C content was 39.4 mol%. Based on these results, it is concluded that strain YYJ7-1^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus shunpengii sp. nov. is proposed, with YYJ7-1^T (=ACCC 19965^T=KCTC 33849^T) as the type strain.

Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas

A Gram-stain-positive, endospore-forming, rod-shaped, aerobic bacterium, designated LPB0068^T, was isolated from a Pacific oyster (Crassostrea gigas) in Korea. This isolate was found to share the highest 16S rRNA gene sequence similarity with Paenibacillus macquariensis subsp. macquariensis DSM 2^T (98.1 %) and Paenibacillus macquariensis subsp. defensor JCM 14954^T (98.0 %). To establish the genomic relatedness of this isolate to its phylogenetic neighbours, its genome sequence and those of Paenibacillus antarcticus CECT 5836^T, P. macquariensis subsp. macquariensis DSM 2^T, P. macquariensis subsp. defensor JCM 14954^T, and Paenibacillus glacialis DSM 22343^T were determined. The low average nucleotide identity and digital DNA-DNA hybridization values exhibited by LPB0068^T in relation to the other strains in this analysis revealed that it is distinct from other Paenibacillus species. The genome of strain LPB0068^T consists of one chromosome and three circular plasmids, and had a DNA G+C content of 40.0 mol%. The major respiratory quinone was menaquinone-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified glycolipid, and two unidentified polar lipids. The major cellular fatty acids were anteiso-C15 : 0, C14 : 0, and C16 : 0. Based on genomic, phylogenetic, and phenotypic characteristics, this strain was clearly distinguished from other Paenibacillus species with validly published names and should therefore be classified as a novel species of the genus. The name Paenibacillus crassostreae sp. nov. is proposed, the type strain of which is LPB0068^T (=KACC 18694^T=JCM 31183^T).

Paenibacillus albidus sp. nov., isolated from grassland soil

A novel bacterial strain, designed Q4-3^T, was isolated from a soil sample obtained from Qilian grassland, Qinghai, China. Phylogenetic, phenotypic, chemotaxonomic and molecular analyses were performed on the new isolate. Cells were Gram-stain-positive, facultatively anaerobic, spore-forming, motile rods with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences placed strain Q4-3^T in the genus Paenibacillus, and its closest relatives were Paenibacillus odorifer JCM 21743^T, Paenibacillus typhae DSM 25190^T, Paenibacillus borealis DSM 13188^T and Paenibacillus etheri DSM 29760^T with 16S rRNA gene sequence similarities of 98.12, 97.89, 97.63 and 97.6 %, respectively. The isolate grew at 4-37 °C (optimum 28-30 °C), at pH 6.0-10.0 (optimum pH 7.5) and with 0-3 %(w/v) NaCl (optimum 1 %). The DNA of strain Q4-3^T was determined to be 48.6 mol%. The predominant menaquinone was MK-7 and the diamino acid in the cell-wall peptidoglycan was found to be meso-diaminopimelic acid. Anteiso-C15 : 0 (55.5 %), iso-C16 : 0 (14.5 %) and C16 : 0 (13.3 %) were the major fatty acids. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified lipid. Based on these results, strain Q4-3^T is considered to represent a novel of the genus Paenibacillus, for which the name Paenibacillusalbidus nov. is proposed. The type strain is Q4-3^T (=CGMCC 1.16134^T=KCTC 33911^T).

Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater

Strain 11^T was isolated from water of an artificial lake accumulating industrial wastewater on the outskirts of Celje, Slovenia. Phenotypic characterisation showed strain 11^T to be a Gram-stain positive, spore forming bacterium. The 16S rRNA gene sequence identified strain 11^T as a member of the genus Paenibacillus, closely related to Paenibacillus alvei (96.2%). Genomic similarity with P. alvei 29^T was 73.1% (gANI), 70.2% (ANIb), 86.7% (ANIm) and 21.7 ± 2.3% (GGDC). The DNA G+C content of strain 11^T was determined to be 47.5%. The predominant menaquinone of strain 11^T was identified as MK-7 and the major fatty acid as anteiso-C_15:0. The peptidoglycan was found to contain meso-diaminopimelic acid. In contrast to its close relatives P. alvei DSM 29^T, Paenibacillus apiarius DSM 5581^T and Paenibacillus profundus NRIC 0885^T, strain 11^T was found to be able to ferment D-fructose, D-mannose and D-xylose. A draft genome of strain 11^T contains a cluster of genes associated with type IV pilin synthesis usually found in clostridia, and only sporadically in other Gram-positive bacteria. Genotypic, chemotaxonomic, physiological and biochemical characteristics of strain 11^T presented in this study support the creation of a novel species within the genus Paenibacillus, for which the name Paenibacillus aquistagni sp. nov. is proposed, with strain 11^T (=ZIM B1027^T =LMG 29561^T =CCM 8679^T ) as the type strain.

Paenibacillus spp. isolated from human and environmental samples in Spain: detection of 11 new species

One hundred thirty-six isolates, 88 human and 48 environmental, that met the requirements to belong to the genus Paenibacillus were identified using a polyphasic taxonomic approach known as 16S rRNA plus phenotypic traits. Thirty-seven Paenibacillus species were identified; some had not been previously reported from clinical samples. The main species were P. pabuli (13 isolates), P. provencensis (11), P. phoenicis (9) and P. lautus (8). P. pabuli (11/13) and P. provencensis (8/11) were mainly environmental isolates, while P. phoenicis (9/9) and P. lautus (6/8) were mainly human isolates. Despite the difficulties in assigning to human Paenibacillus isolates a role as a pathogen or contaminant, here 25% of the isolates were involved in true infections, especially in those cases that affected abscesses, wound exudates, ocular infections and diverse fluids. In addition, 15 isolates were identified as 11 'Candidatus' to a new species, all of them from human specimens except one that was obtained from laboratory air. The antimicrobial susceptibility testing showed 95.6% of isolates were resistant to ampicillin, 44% were resistant to cotrimoxazole, 20 to 30% were resistant to cefotaxime and vancomycin and 13% were resistant to rifampicin and erythromycin.

Current knowledge and perspectives of Paenibacillus: a review

Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.

Intraoperative diagnosis of mitral valve endocarditis secondary to Paenibacillus provencensis

We report the first case of infective endocarditis caused by Paenibacillus provencensis. A mitral valve vegetation was incidentally discovered by intraoperative transoesophageal echocardiography in a 70-year-old woman undergoing aortic valve replacement. The precise identification of the causative agent was by means of genotypic characterisation with 16S rDNA gene sequencing. The patient was successfully treated with a 6-week course of antibiotics postoperatively, following debridement of the valve vegetation.

High-quality genome sequence and description of Paenibacillus dakarensis sp. nov

Strain FF9T was isolated in Dakar (Senegal) from a blood-culture taken from a 16-month-old child. MALDI-TOF analysis did not allow for identification. After sequencing, strain FF9T exhibited 98.18% similarity with the 16SrRNA sequence of Paenibacillus uliginis. A polyphasic study of phenotypic and genomic analyses showed that strain FF9T is Gram variable, catalase-positive, and presents a genome of 4,569,428 bp (one chromosome but no plasmid) with 4,427genes (4,352 protein-coding and 75 RNA genes (including 3 rRNA operons). The G+C content is 45.7%. On the basis of these genomic and phenotypic data analyses, we propose the creation of Paenibacillus dakarensis strain FF9T.

Paenibacillus medicaginis sp. nov. a chitinolytic endophyte isolated from a root nodule of alfalfa (Medicago sativa L.)

A Gram-stain-variable, short-rod-shaped, endospore-forming, strictly aerobic, non-motile, chitinolytic and endophytic bacterium, designated strain CC-Alfalfa-19T, exhibiting unusual bipolar appendages was isolated from a root nodule of alfalfa (Medicago sativa L.) in Taiwan and subjected to a polyphasic taxonomic study. Based on 16S rRNA gene sequence analysis, strain CC-Alfalfa-19T was found to be most closely related to Paenibacillus puldeungensis CAU 9324T (95.2 %), whereas other species of the genus Paenibacillus shared ≤ 95.0 % sequence similarity. The phylogenetic analysis revealed a distinct phyletic lineage established by strain CC-Alfalfa-19T with respect to other species of the genus Paenibacillus. Fatty acids comprised predominantly anteiso-C15 : 0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0. Menaquinone 7 (MK-7) was identified as the sole respiratory quinone and the genomic DNA G+C content was 42.7 mol%. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on the polyphasic taxonomic evidence that was in line with the genus Paenibacillus and additional distinguishing characteristics, strain CC-Alfalfa-19T is considered to represent a novel species, for which the name Paenibacillus medicaginis sp. nov. (type strain CC-Alfalfa-19T = BCRC 80441T = JCM 18446T) is proposed.

Molecular characterization of forest soil based Paenibacillus elgii and optimization of various culture conditions for its improved antimicrobial activity

Microorganisms have provided a bounty of bioactive secondary metabolites with very exciting biological activities such as antibacterial, antifungal antiviral, and anticancer, etc. The present study aims at the optimization of culture conditions for improved antimicrobial production of Paenibacillus elgii obtained from Wayanad forest of Western Ghats region of Kerala, India. A bacterial strain isolated from the Western Ghats forest soil of Wayanad, Kerala, India was identified as P. elgii by 16S rRNA gene sequencing. P. elgii recorded significant board spectrum activity against all human and plant pathogenic microorganism tested except Candida albicans. It has been well known that even minor variations in the fermentation medium may impact not only the quantity of desired bioactive metabolites but also the general metabolic profile of the producing microorganisms. Thus, further studies were carried out to assess the impact of medium components on the antimicrobial production of P. elgii and to optimize an ideal fermentation medium to maximize its antimicrobial production. Out of three media [nutrient broth (NA), Luria broth (LB) and Trypticase soy broth (TSB)] used for fermentation, TSB medium recorded significant activity. Glucose and meat peptone were identified as the best carbon and nitrogen sources, which significantly affected the antibiotic production when supplemented with TSB medium. Next the effect of various fermentation conditions such as temperature, pH, and incubation time on the production of antimicrobial compounds was studied on TSB + glucose + meat peptone and an initial pH of 7 and a temperature of 30°C for 3 days were found to be optimum for maximum antimicrobial production. The results indicate that medium composition in the fermentation media along with cultural parameters plays a vital role in the enhanced production of antimicrobial substances.

Paenibacillus rhizoryzae sp. nov., isolated from rice rhizosphere

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated 1ZS3-5T, was isolated from rice rhizosphere in Hunan Province, PR China. The isolate was identified as a member of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference analysis. The 16S rRNA and rpoB gene (β-subunit of bacterial RNA polymerase) sequences were closely related to those of Paenibacillus taihuensis CGMCC 1.10966T with similarities of 97.2 % and 89.7 %, respectively. The DNA–DNA hybridization value between 1ZS3-5T and P. taihuensis CGMCC 1.10966T was 33.4 %. The DNA G+C content of 1ZS3-5T was 47.5 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipid and unknown phospholipid. The predominant respiratory quinone was MK-7. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. Based on these results, 1ZS3-5T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus rhizoryzae sp. nov. is proposed. The type strain is 1ZS3-5T ( = ACCC 19782T = DSM 29322T).

Paenibacillus insulae sp. nov., isolated from soil

A Gram-stain-positive, motile, endospore-forming, and strictly aerobic rod-shaped bacterium designated DS80(T) was isolated from an island soil. The strain DS80(T) grew at temperatures between 15 and 40°C (optimum = 30°C) and at pH values ranging from 5.0 to 9.0 (optimum = 7.0). The phylogenetic analysis based on the comparisons of the 16S rRNA gene sequences showed that the isolate was affiliated to the genus Paenibacillus and was mostly related to Paenibacillus assamensis GPTSA11(T) (with the sequence similarity of 96.33%) and Paenibacillus urinalis 5402403(T)(95.48%). The G+C content of the genomic DNA was 44.0 mol% and the major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0, and C16:1 ω11c. Strain DS80(T) contained MK-7 as the major menaquinone, and phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol as the major polar lipids. The peptidoglycan contained a major amount of meso-diaminopimelic acid. The chemotaxonomic profile of strain DS80(T) was consistent with that of Paenibacillus. However, the phenotypic properties clearly separated the strain from other species of the genus. Accordingly, a new species, Paenibacillus insulae sp. nov., is proposed (type strain =DS80(T) =JCM 17278(T) =KCTC 13833(T)).

Paenibacillus physcomitrellae sp. nov., isolated from the moss Physcomitrella patens

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain XBT, was isolated from Physcomitrella patens growing in Beijing, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inferences. The novel strain was spore-forming, motile, catalase-negative and weakly oxidase-positive. Optimal growth of strain XBT occurred at 28°C and pH 7.0-7.5. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unidentified components, including one phospholipid, two aminophospholipids, three glycolipids, one aminolipid and one lipid. The predominant isoprenoid quinone was MK-7. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acid components (>5 %) were anteiso-C15 : 0 (51.2 %), anteiso-C17 : 0 (20.6 %), iso-C16 : 0 (8.3 %) and C16 : 0 (6.7 %). The G+C content of the genomic DNA was 53.3 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain XBT fell within the evolutionary distances encompassed by the genus Paenibacillus; its closest phylogenetic neighbour was Paenibacillus yonginensis DCY84T (96.6 %). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain XBT is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus physcomitrellae sp. nov., is proposed. The type strain is XBT ( = CGMCC 1.15044T = DSM 29851T).

A Case of Paenibacillus pasadenensis Bacteremia in a Patient with Acute Respiratory Distress Syndrome after Microsurgical Clipping

We report the first case of bacteremia by a novel Paenibacillus species, Paenibacillus pasadenensis, from a 55-year-old male patient with acute respiratory distress syndrome, following a microsurgical clipping procedure of a ruptured intracranial aneurysm. The bacterium was identified using 16S rRNA gene sequencing analysis, which was applied because current conventional methods employed in the clinical microbiology laboratory proved unsuccessful. Since this bacterium was first identified in 2006 and has never been reported elsewhere, we believe this report can provide practitioners with useful insight on the pathogenicity of this species.

Detecting the dormant: a review of recent advances in molecular techniques for assessing the viability of bacterial endospores

Due to their contribution to gastrointestinal and pulmonary disease, their ability to produce various deadly exotoxins, and their resistance to extreme temperature, pressure, radiation, and common chemical disinfecting agents, bacterial endospores of the Firmicutes phylum are a major concern for public and environmental health. In addition, the hardy and dormant nature of endospores renders them a particularly significant threat to the integrity of robotic extraterrestrial life-detection investigations. To prevent the contamination of critical surfaces with seemingly ubiquitous bacterial endospores, clean rooms maintained at exceedingly stringent cleanliness levels (i.e., fewer than 100,000 airborne particles per ft(3)) are used for surgical procedures, pharmaceutical processing and packaging, and fabrication and assembly of medical devices and spacecraft components. However, numerous spore-forming bacterial species have been reported to withstand typical clean room bioreduction strategies (e.g., UV lights, maintained humidity, paucity of available nutrients), which highlights the need for rapid and reliable molecular methods for detecting, enumerating, and monitoring the incidence of viable endospores. Robust means of evaluating and tracking spore burden not only provide much needed information pertaining to endospore ecophysiology in different environmental niches but also empower decontamination and bioreduction strategies aimed at sustaining the reliability and integrity of clean room environments. An overview of recent molecular advances in detecting and enumerating viable endospores, as well as the expanding phylogenetic diversity of pathogenic and clean room-associated spore-forming bacteria, ensues.

Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain xj7T, was isolated from roots of Typha angustifolia L. growing in Beijing Cuihu Wetland, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inference. The novel strain was spore-forming, motile, catalase-positive and oxidase-negative. Optimal growth of strain xj7T occurred at 28–30 °C and pH 7.0–7.5. Diphosphatidylglycerol was the most abundant polar lipid and occurred along with phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and three unknown aminophospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant isoprenoid quinone was MK-7. The major fatty acid components were anteiso-C15 : 0 (56.1 %), iso-C16 : 0 (9.1 %), C16 : 0 (8.0 %), iso-C14 : 0 (6.3 %) and iso-C15 : 0 (5.1 %). The G+C content of genomic DNA was 47.9 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain xj7T fell within the evolutionary radiation encompassed by the genus Paenibacillus , its closest neighbours were Paenibacillus borealis KK19T (97.5 %) and Paenibacillus durus DSM 1735T (97.1 %). However, the DNA–DNA relatedness values between strain xj7T and P. borealis KK19T and between strain xj7T and P. durus DSM 1735T, were both 35 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain xj7T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus typhae sp. nov. is proposed. The type strain is xj7T ( = CGMCC 1.11012T = DSM 25190T).

Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing

Psychrotolerant spore-forming bacteria represent a major challenge to the goal of extending the shelf life of pasteurized dairy products. The objective of this study was to identify prominent phylogenetic groups of dairy-associated aerobic sporeformers and to characterize representative isolates for phenotypes relevant to growth in milk. Analysis of sequence data for a 632-nucleotide fragment of rpoB showed that 1,288 dairy-associated isolates (obtained from raw and pasteurized milk and from dairy farm environments) clustered into two major divisions representing (i) the genus Paenibacillus (737 isolates, including the species Paenibacillus odorifer, Paenibacillus graminis, and Paenibacillus amylolyticus sensu lato) and (ii) Bacillus (n = 467) (e.g., Bacillus licheniformis sensu lato, Bacillus pumilus, Bacillus weihenstephanensis) and genera formerly classified as Bacillus (n = 84) (e.g., Viridibacillus spp.). When isolates representing the most common rpoB allelic types (ATs) were tested for growth in skim milk broth at 6°C, 6/9 Paenibacillus isolates, but only 2/8 isolates representing Bacillus subtypes, grew >5 log CFU/ml over 21 days. In addition, 38/40 Paenibacillus isolates but only 3/47 Bacillus isolates tested were positive for β-galactosidase activity (including some isolates representing Bacillus licheniformis sensu lato, a common dairy-associated clade). Our study confirms that Paenibacillus spp. are the predominant psychrotolerant sporeformers in fluid milk and provides 16S rRNA gene and rpoB subtype data and phenotypic characteristics facilitating the identification of aerobic spore-forming spoilage organisms of concern. These data will be critical for the development of detection methods and control strategies that will reduce the introduction of psychrotolerant sporeformers and extend the shelf life of dairy products.

Paenimacrolidin, a novel macrolide antibiotic from Paenibacillus sp. F6-B70 active against methicillin-resistant Staphylococcus aureus

Paenibacillus sp. F6-B70 was selected from several dozens of isolates with activity against methicillin-resistant Staphylococcus aureus using a 16S rDNA-based screening method. F6-B70 contained polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) clusters in its genome revealed by PCR amplification of conserved adenylation and ketosynthase (KS) domains. Phylogenetic data suggested that the strain hosts trans-AT PKSs and their product may be a branched molecule. An antibiotic was subsequently isolated from the methanol extract of F6-B70 cells. The molecular formula of the antibiotic was deduced to be C(33) H(50) NaO(6) ([M + Na](+) , m/z 565.3505) by analysis of electrospray ionization mass spectral data. Elucidation of the structure by nuclear magnetic resonance and infrared spectroscopy revealed that the active compound, paenimacrolidin (PAM), was a novel 22-membered macrolide with side-chains. The new antibiotic, mainly as a bacteriostatic agent, inhibits a couple of multidrug-resistant Staphylococcus sp. strains. The antibiotic capacity of PAM was compromised by its instability, which can be overcome significantly with addition of an anti-oxidant. To our knowledge, this is the first report of the isolation of an active macrolide from paenibacilli, which may be a promising source of novel antibiotics.

Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).

Paenibacillus algorifonticola sp. nov., isolated from a cold spring

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259(T), was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20-30 °C and pH 7.3-7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259(T) belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538(T) (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1(T) (96.3 %) and Paenibacillus castaneae Ch-32(T) (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C₁₅:₀ and C₁₆:₀ as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259(T) ( = CGMCC 1.10223(T)  = JCM 16598(T)).

Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease

Strain KIT 00200-70066-1(T) was isolated from the sputum of a patient with pulmonary disease. Cells of the strain were Gram-variable, facultatively anaerobic, motile, spore-forming rods and formed colourless to white colonies on tryptic soy agar at 30&emsp14;°C and pH&emsp14;7. The pathogenicity of the strain is not known. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, anteiso-C₁₅:₀, iso-C₁₆:₀ and C₁₆:₀ as the major fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus nanensis MX2-3(T), Paenibacillus agaridevorans DSM 1355(T) and Paenibacillus alkaliterrae KSL-134(T) (95.4, 95.2 and 94.8 %, respectively), and that it occupied a distinct position within this genus. Combined phylogenetic and phenotypic data supported the conclusion that strain KIT 00200-70066-1(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sputi sp. nov. is proposed; the type strain is KIT 00200-70066-1(T) (=KCTC 13252(T) =DSM 22699(T)).