The anti-infective potential of the endophytic fungi associated with Allium cepa supported by metabolomics analysis and docking studies.

Endophytic fungi are known to be a rich source of anti-infective drugs. In our study, Allium cepa was investigated for fungal diversity using different media to give 11 isolates which were identified morphologically. Out of the isolated fungal strains, Penicillium sp. (LCEF10) revealed potential anti-infective activity against the tested microbes (Fusarium solani ATTC 25922, Pseudomonas aeruginosa (ATTC 29231), Staphylococcus aureus ATTC 27853, Candida albicans ATTC 10231), besides, their MICs were measured by well diffusion method, therefore, it was subjected to molecular identification in addition to phylogenetic analysis. Moreover, the ITS sequence of strain LCEF10 showed a consistent assignment with the highest sequence similarity (99.81%) to Penicillium oxalicum NRRL 787. The crude ethyl acetate extract of Penicillium sp. LCEF10 was investigated for metabolomic analysis using LC-HR-ESI-MS. The metabolic profiling revealed the presence of polyketides, macrolides, phenolics and terpenoids. Furthermore, in silico molecular docking study was carried out to predict which compounds most likely responsible for the anti-infective activity.

High diversity of the emerging pathogen Acinetobacter baumannii and other Acinetobacter spp. in raw manure, biogas plants digestates, and rural and urban wastewater treatment plants with system specific antimicrobial resistance profiles.

Carbapenem-resistant Acinetobacter baumannii causing immense treatment problems in hospitals. There is still a knowledge gap on the abundance and stability of acquired resistances and the diversity of resistant Acinetobacter in the environment. The aim of the study was to investigate the diversity and antimicrobial resistances of Acinetobacter spp. released from livestock and human wastewater into the environment. Raw and digested manure of small scale on farm biogas plants as well as untreated and treated wastewater and sewage sludge of rural and urban wastewater treatment plants (WWTPs) were studied comparatively. A total of 132 Acinetobacter isolates were phylogenetically identified (16S rRNA gene and rpoB sequence analyses) and 14 different phylotypes were detected. Fiftytwo isolates represented A. baumannii which were cultured from raw and digested manure of different biogas plants, and most stages of the rural WWTP (no hospital wastewater receiving) and the two studied urban WWTPs receiving veterinarian and human hospital wastewater. Multi-locus sequence typing (Pasteur_MLST) identified 23 novel and 12 known STs of A. baumannii. Most novel STs (18/23) were cultured from livestock samples and the rural WWTP. A. baumannii isolates from livestock and the rural WWTP were susceptible to carbapenems, colistin, ciprofloxacin, ceftazidime, and piperacillin. In contrast, A. baumannii isolates from the two urban WWTPs showed clinical linkage with respect to MLST and were multi-drug resistant (MDR). The presence of viable A. baumannii in digested manure and sewage sludge confirmed the survival of the strict aerobic bacteria during anoxic conditions. The study indicated the spread of diverse Acinetobacter from anthropogenic sources into the environment with a strong linkage of clinial associated MDR A. baumannii strains to the inflow of hospital wastewater to WWTPs. A more frequent detection of Acinetobacter in sewage sludge than effluent waters indicated that particle-attachment of Acinetobacter must be considered by the risk assessment of these bacteria.

Jeotgalicoccus schoeneichii sp. nov. isolated from exhaust air of a pig barn.

A Gram-staining-positive, non-motile, non-spore-forming, coccus (strain 140805-STR-02T) was isolated from exhaust air of a pig barn on Columbia Blood Agar Base (Oxoid) supplemented with 5 % defibrinated horse blood, Streptococcus selective supplement and 0.5 mg erythromycin l-1. The strains shared high 16S rRNA gene sequence similarity to Jeotgalicoccus pinnipedialis (98.6 %) but only a maximum of 94 % sequence similarity to all other species of the genus Jeotgalicoccus. DNA-DNA hybridisation values between strain 140805-STR-02T and J. pinnipedialis CIP 107946T were 60.3 % (reciprocal, 51.2 %). The quinone system of 140805-STR-02T contained predominantly menaquinone MK-7 and minor amounts of MK-6. The polar lipid profile of strain 140805-STR-02T contained the major compounds diphosphatidylglycerol and phosphatidylglycerol and four unidentified lipids present in minor to moderate amounts. In the polyamine pattern spermidine and spermine were predominant. The fatty acid profile comprising iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids, and was in congruence with those reported for other species of the genus Jeotgalicoccus and thus supported the affiliation of strain 140805-STR-02T to this genus. The results of physiological and biochemical tests allowed a clear phenotypic differentiation of strain 140805-STR-02T from the most closely related species. Strain 140805-STR-02T represents a novel species, for which the names Jeotgalicoccus schoeneichii sp. nov. is proposed, with the type strain 140805-STR-02T (=LMG 29445T=CCM 8667T).

Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations.

Strain BCT-7112(T) was isolated in 1966 in Japan from a survey designed to obtain naturally occurring microorganisms as pure cultures in the laboratory for use as probiotics in animal nutrition. This strain, which was primarily identified as Bacillus cereus var toyoi, has been in use for more than 30 years as the active ingredient of the preparation TOYOCERIN(®), an additive for use in animal nutrition (e.g. swine, poultry, cattle, rabbits and aquaculture). Despite the fact that the strain was initially classified as B. cereus, it showed significant genomic differences from the type strains of the B. cereus group that were large enough (ANI values below 92%) to allow it to be considered as a different species within the group. The polyphasic taxonomic study presented here provides sufficient discriminative parameters to classify BCT-7112(T) as a new species for which the name Bacillus toyonensis sp. nov. is proposed, with BCT-7112(T) (=CECT 876(T); =NCIMB 14858(T)) being designated as the type strain. In addition, a pairwise comparison between the available genomes of the whole B. cereus group by means of average nucleotide identity (ANI) calculations indicated that besides the eight classified species (including B. toyonensis), additional genomospecies could be detected, and most of them also had ANI values below 94%. ANI values were on the borderline of a species definition only in the cases of representatives of B. cereus versus B. thuringiensis, and B. mycoides and B. weihenstephanensis.

Niabella hirudinis and Niabella drilacis sp. nov., isolated from the medicinal leech Hirudo verbana.

Two Gram-negative, rod-shaped bacteria, strains E96(T) and E90(T), were isolated from medicinal leeches (Hirudo verbana) and characterized by a polyphasic taxonomic approach. Phylogenetic analysis based on the nearly full-length 16S rRNA gene sequence showed that the two strains shared 98.1% sequence similarity and were affiliated with the genus Niabella within the phylum Bacteroidetes, with 94.4-97.6% sequence similarity to type strains of species of the genus Niabella and highest sequence similarity to the type strain of Niabella aurantiaca (97.3 and 97.6%, respectively). Niabella-related 16S rRNA gene sequences were recently detected in the bladders of Hirudo verbana; however, no cultured representatives were so far available. Genomic fingerprint analysis using repetitive element primed (rep)- and randomly amplified polymorphic DNA (RAPD)-PCRs and DNA-DNA hybridization experiments clearly showed that the strains were different from each other (DNA-DNA relatedness values of 39.1%, reciprocal 28.0%) and from the type strains of N. aurantiaca (<19.7%) and Niabella tibetensis (<41.1%). Chemotaxonomic analyses confirmed the affiliation to the genus Niabella. Both strains contained MK-7 as the predominant menaquinone. The major fatty acids of both strains were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH), which is characteristic for the genus Niabella. Based on genotypic, chemotaxonomic and physiological characterization, we propose two novel species of the genus Niabella, Niabella hirudinis sp. nov., with strain E96(T) ( =DSM 25812(T) =CCM 8411(T) =LMG 26956(T)) as the type strain, and Niabella drilacis sp. nov., with strain E90(T) ( =DSM 25811(T) =CCM 8410(T) =LMG 26954(T)) as the type strain.

Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment.

Two Gram-negative, rod-shaped, non-spore-forming bacteria, PR17(T) and DSM 7216(T), isolated from the potato rhizosphere and an industrial environment, respectively, were studied for their taxonomic allocation. By rrs (16S rRNA) gene sequencing, these strains were shown to belong to the Alphaproteobacteria, most closely related to Ochrobactrum pseudogrignonense (98.4 and 99.3 % similarity to the type strain, respectively). Chemotaxonomic data (major ubiquinone Q-10; major polyamines spermidine, sym-homospermidine and putrescine; major polar lipids phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and the Ochrobactrum-specific unidentified aminolipid AL2; major fatty acids C(18 : 1)omega7c and C(19 : 0) cyclo omega8c) supported the genus affiliation. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from all hitherto-described Ochrobactrum species. Hence, both isolates represent novel species of the genus Ochrobactrum, for which the names Ochrobactrum rhizosphaerae sp. nov. (type strain PR17(T) =CCUG 55411(T) =CCM 7493(T) =DSM 19824(T)) and Ochrobactrum thiophenivorans sp. nov. (type strain DSM 7216(T) =CCUG 55412(T) =CCM 7492(T)) are proposed.

Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site.

A Gram-negative, rod-shaped bacterium (CC-JY-1(T)) was isolated on nutrient agar from a soil sample collected from an oil-contaminated site located in Chyai county, Taiwan. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing 96.7 % sequence similarity to the type strain of Arenimonas donghaensis and similarities of 93.0-93.8 % to species of the genera Thermomonas, Lysobacter and Silanimonas. The presence of ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and the fatty acid profile were in accordance with the phylogenetic affiliation of CC-JY-1(T). DNA-DNA reassociation experiments between CC-JY-1(T) and A. donghaensis KACC 11381(T) resulted in a mean relatedness value of 32 %, indicating that strain CC-JY1(T) represents a novel species in the genus Arenimonas, for which we propose the name Arenimonas malthae sp. nov. The type strain is CC-JY-1(T) (=CCUG 53596(T) =CIP 109310(T)).