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1.
Vavilovskii Zhurnal Genet Selektsii ; 28(3): 308-316, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38952705

ABSTRACT

We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.

2.
Article in English | MEDLINE | ID: mdl-39008344

ABSTRACT

Gram-stain-positive, aerobic, rod-shaped strains, YJM1T and YJM12S, were isolated from Maebong Mountain, Dogok-dong, Gangnam-gu, Seoul, Republic of Korea. Strains YJM1T and YJM12S exhibited growth at 5-35 °C (optimum, 20-30 °C) and pH 6-9 (optimum, pH 7) and in 0-4 % (w/v) NaCl. Strains YJM1T and YJM12S showed highest 16S rRNA gene sequence similarity to the following members of the genus Arthrobacter: A. nanjingensis A33T (98.3 %/98.2 % similarity), A. woluwensis NBRC 107840T (98.2 %/98.1 %), A. humicola KV-653T (97.3 %), A. oryzae KV-651T (97.3 %), and A. globiformis NBRC 12137T (97.2 %). The strains grew well on Reasoner's 2A, nutrient, Mueller-Hinton, yeast-dextrose, and glucose-peptone-meat extract agars. The major polar lipids of strain YJM1T were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The primary respiratory quinone of strain YJM1T was MK-9(H2), and the major fatty acids of strains YJM1T and YJM12S were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, and iso-C16 : 0. The DNA G+C content, based on the whole genome sequence of strain YJM1T, was 68.3 mol%. Average nucleotide identity values and digital DNA-DNA hybridization values between strain YJM1T and the reference strains ranged from 75.0 to 92.7 % and from 21.0 to 65.3 %, respectively. Strain YJM1T exhibited antimicrobial activity against Bacillus subtilis and Escherichia coli. Considering the chemotaxonomic, phenotypic, genotypic, and phylogenetic results, we propose the strain YJM1T represents a novel species in the genus Arthrobacter and suggest the name Arthrobacter horti sp. nov. (type strain YJM1T=KACC 23300T=JCM 36483T).


Subject(s)
Arthrobacter , Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Soil Microbiology , Vitamin K 2 , Arthrobacter/genetics , Arthrobacter/classification , Arthrobacter/isolation & purification , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , DNA, Bacterial/genetics , Republic of Korea , Vitamin K 2/analogs & derivatives , Phospholipids/chemistry , Seoul
3.
Appl Microbiol Biotechnol ; 108(1): 325, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38717668

ABSTRACT

Actinomycetota have been widely described as valuable sources for the acquisition of secondary metabolites. Most microbial metabolites are produced via metabolic pathways encoded by biosynthetic gene clusters (BGCs). Although many secondary metabolites are not essential for the survival of bacteria, they play an important role in their adaptation and interactions within microbial communities. This is how bacteria isolated from extreme environments such as Antarctica could facilitate the discovery of new BGCs with biotechnological potential. This study aimed to isolate rare Actinomycetota strains from Antarctic soil and sediment samples and identify their metabolic potential based on genome mining and exploration of biosynthetic gene clusters. To this end, the strains were sequenced using Illumina and Oxford Nanopore Technologies platforms. The assemblies were annotated and subjected to phylogenetic analysis. Finally, the BGCs present in each genome were identified using the antiSMASH tool, and the biosynthetic diversity of the Micrococcaceae family was evaluated. Taxonomic annotation revealed that seven strains were new and two were previously reported in the NCBI database. Additionally, BGCs encoding type III polyketide synthases (T3PKS), beta-lactones, siderophores, and non-ribosomal peptide synthetases (NRPS) have been identified, among others. In addition, the sequence similarity network showed a predominant type of BGCs in the family Micrococcaceae, and some genera were distinctly grouped. The BGCs identified in the isolated strains could be associated with applications such as antimicrobials, anticancer agents, and plant growth promoters, among others, positioning them as excellent candidates for future biotechnological applications and innovations. KEY POINTS: • Novel Antarctic rare Actinomycetota strains were isolated from soil and sediments • Genome-based taxonomic affiliation revealed seven potentially novel species • Genome mining showed metabolic potential for novel natural products.


Subject(s)
Geologic Sediments , Multigene Family , Phylogeny , Soil Microbiology , Antarctic Regions , Geologic Sediments/microbiology , Secondary Metabolism/genetics , Actinobacteria/genetics , Actinobacteria/metabolism , Actinobacteria/classification , Genome, Bacterial , Biotechnology/methods , Biosynthetic Pathways/genetics , Peptide Synthases/genetics , Peptide Synthases/metabolism , Polyketide Synthases/genetics , Polyketide Synthases/metabolism
4.
Arch Microbiol ; 206(4): 165, 2024 Mar 14.
Article in English | MEDLINE | ID: mdl-38485793

ABSTRACT

This article reports the results of quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains and a novel endophytic bacterium (SG) isolated from a suspension culture of Arabidopsis thaliana (L.) Heynh in our laboratory. The known strain Rothia sp. ND6WE1A was used as a reference one for SG. Whole-genome sequencing and phylogenetic analysis were based on the 16S rRNA test. Quantitative analysis for the nucleotide identity (ANI) and calculation of evolutionary distances were based on the identified amino acids (AAI) test indicating the generic assignment of the reference strain within and between the identified monophyletic groups of Micrococcaceae. The amino acid data structure of Rothia sp. ND6WE1A was compared against the UniProt database (250 million records) of close lineage of Micrococcaceae, including other Rothia spp. These data presented unique and evolutionary amino acid alignments, eventually expected in the new SG isolate as well. The metagenomic entries of the respective genome and proteome, characterized at the genus and species levels, could be considered for evolutionary taxonomic reclassification of the isolated and the reference strain (SG + Rothia sp. ND6WE1A). Therefore, our results warrant further investigations on the isolated SG strain.


Subject(s)
Micrococcaceae , Micrococcaceae/genetics , Phylogeny , Fatty Acids/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Base Composition , Amino Acids/metabolism , Bacterial Typing Techniques , Nucleic Acid Hybridization
5.
Chemosphere ; 340: 139761, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37558001

ABSTRACT

BTEX (benzene, toluene, ethylbenzene, xylene) are common pollutants often found in former gasworks sites together with some other contaminants like indene, indane and naphthalene (Ie, Ia, N). This study aimed to evaluate the inhibitory or stimulative substrate interactions between BTEX, and Ie, Ia, N during aerobic biodegradation. For this, batch bottles, containing originally anaerobic subsurface sediments, groundwater and indigenous microorganisms from a contaminated former gasworks site, were spiked with various substrate combinations (BTEX, BTEXIe, BTEXIa, BTEXN, BTEXIeIa, BTEXIeN, BTEXIaN, BTEXIeIaN). Subsequently concentrations were monitored over time. For the BTEXIeIaN mixture, initial concentrations were between 1 and 5 mg L-1, and all compounds were completely degraded by the microbial consortia within 39 days of incubation. The experimental data were fitted to a first order kinetic degradation model for interpretation of inhibition/stimulation between the compounds. Results showed that indene, indane, and naphthalene inhibited the degradation of benzene, toluene, ethylbenzene, o-xylene, with benzene being the most affected. M/p-xylene is the only compound whose biodegradation is stimulated by the presence of indene and indane (individually or mixed) but inhibited by the presence of naphthalene. 16S rRNA amplicon sequencing revealed differentiation in the microbial communities within the batches with different substrate mixtures, especially within the two microbial groups Micrococcaceae and Commamonaceae. Indene had more effect on the BTEX microbial community than indane or naphthalene and the presence of indene increased the relative abundance of Micrococcaceae family. In conclusion, co-presence of various pollutants leads to differentiation in degradation processes as well as in microbial community development. This sheds some light on the underlying reasons for that organic compounds present in mixtures in the subsurface of former gasworks sites are either recalcitrant or subjective towards biodegradation, and this understanding helps to further improve the bioremediation of such sites.


Subject(s)
Environmental Pollutants , Indenes , Microbiota , Benzene/chemistry , Biodegradation, Environmental , Kinetics , RNA, Ribosomal, 16S/genetics , Benzene Derivatives/chemistry , Xylenes/metabolism , Toluene/chemistry , Naphthalenes
6.
J Clin Microbiol ; 61(4): e0148422, 2023 04 20.
Article in English | MEDLINE | ID: mdl-36946723

ABSTRACT

Rothia, Kocuria, Arthrobacter, and Pseudoglutamicibacter are bacterial species within the family Micrococcaeae. Knowledge of human infections due to these bacteria is limited. This study aimed to examine features of infections caused by non-Micrococcus Micrococcaeae (NMM). Findings of NMM from blood cultures and other sterile cultures from 2012 to 2021 were identified from the records of the Department of Clinical Microbiology in Region Skåne, Lund, Sweden. Medical records were retrospectively reviewed. True infection was defined as having signs of infection, no other more likely pathogen, and no other focal infection, together with two positive blood cultures or one positive blood culture and an intravascular device. A total of 197 patients with findings of NMM in blood cultures were included. Among adult patients with bacteremia, 29 patients (22%) were considered to have a true infection. Adults with true infection were significantly more likely to have malignancy (69%), leukopenia (62%), and treatment with chemotherapeutics (66%) compared to patients with contaminated samples (24%, 3%, and 8%, respectively) (P < 0.001). A total of 31 patients had findings of NMM in other sterile cultures, and infections were considered true in joints (n = 4), a pacemaker (n = 1), and peritoneal dialysis fluid (n = 1). Infections due to NMM occur but are rare. Growth of NMM in blood cultures should be suspected to be a true infection mainly in immunocompromised patients.


Subject(s)
Arthrobacter , Bacteremia , Micrococcaceae , Adult , Humans , Micrococcus , Retrospective Studies , Bacteremia/microbiology
7.
Int J Syst Evol Microbiol ; 72(10)2022 Oct.
Article in English | MEDLINE | ID: mdl-36256564

ABSTRACT

An aerobic, Gram-stain-positive and non-spore-forming strain, designated C1-1T, was isolated from a fellfield soil sample collected from frost-sorted polygons on Jane Col, Signy Island, Maritime Antarctic. Cells with a size of 0.65-0.9×1.2-1.7 µm have a flagellar motile apparatus and exhibit a rod-coccus growth cycle. Optimal growth conditions were observed at 15-20 °C, pH 7.0 and NaCl concentration up to 0.5 % (w/v) in the medium. The 16S rRNA gene sequence of C1-1T showed the highest pairwise similarity of 98.77 % to Arthrobacter glacialis NBRC 113092T. Phylogenetic trees based on the 16S rRNA and whole-genome sequences revealed that strain C1-1T belongs to the genus Arthrobacter and is most closely related to members of the 'Arthrobacter psychrolactophilus group'. The G+C content of genomic DNA was 58.95 mol%. The original and orthologous average nucleotide identities between strain C1-1T and A. glacialis NBRC 113092T were 77.15 % and 77.38 %, respectively. The digital DNA-DNA relatedness values between strain C1-1T and A. glacialis NBRC 113092T was 21.6 %. The polar lipid profile was composed mainly of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The predominant cellular fatty acids were anteiso-C15 : 0 (75 %) and anteiso-C17 : 0 (15.2 %). Menaquinone MK-9(H2) (86.4 %) was the major respiratory quinone in strain C1-1T. The peptidoglycan type was determined as A3α (l-Lys-l-Ala3; A11.6). Based on all described phylogenetic, physiological and chemotaxonomic characteristics, we propose that strain C1-1T (=DSM 112353T=CCM 9148T) is the type strain of a novel species Arthrobacter polaris sp. nov.


Subject(s)
Arthrobacter , Micrococcaceae , RNA, Ribosomal, 16S/genetics , Peptidoglycan/chemistry , Phylogeny , Base Composition , Soil , Vitamin K 2/chemistry , Sodium Chloride , Cardiolipins , Antarctic Regions , DNA, Bacterial/genetics , Bacterial Typing Techniques , Fatty Acids/chemistry , Sequence Analysis, DNA , Phospholipids/chemistry , Nucleic Acid Hybridization , Glycolipids/chemistry , Phosphatidylinositols , Nucleotides
8.
IDCases ; 27: e01459, 2022.
Article in English | MEDLINE | ID: mdl-35242563

ABSTRACT

Rothia aeria is a gram-positive, pleomorphic bacteria forming part of human oral microflora usually only causing periodontal and dental infections. We describe the case of a 68-year-old immunocompetent male with lumbar vertebral discitis/osteomyelitis caused by R. aeria. A review of the literature demonstrated seventeen cases of non-dental R. aeria infection of which only six were in immunocompetent individuals. This is the first reported case of R. aeria vertebral discitis/osteomyelitis.

9.
Microorganisms ; 9(7)2021 Jun 25.
Article in English | MEDLINE | ID: mdl-34202256

ABSTRACT

Sliced ready-to-eat meat products packaged under modified atmospheres are often marketed since they cover consumer demands. The slicing process could be a potential risk for consumers since contamination with Listeria monocytogenes could occur during this stage. The current study evaluated the behavior of L. monocytogenes and other microorganisms in commercial sliced Riojano chorizo. This meat product was sliced and inoculated with L. monocytogenes (3.5 log CFU/g) before packaging under different atmospheres (air, vacuum, 100% N2, 20% CO2/80% N2 and 40% CO2/60% N2) and stored at 4 °C for up to 60 days. Samples were taken on days 0, 7, 21, 28 and 60 of storage. L. monocytogenes, mesophiles, Enterobacteriaceae, lactic acid bacteria, Micrococcaceae, molds and yeast counts were evaluated. Additionally, water activity, humidity and pH were determined. L. monocytogenes counts decreased in inoculated sliced chorizo during storage. Packaging conditions and day of storage influenced microbial counts. After 60 days, a significant reduction (p ≤ 0.05) in the initial Listeria contamination levels (3.5. log CFU/g) between 1.1 and 1.46 logarithmic units was achieved in the sausages packaged in modified atmosphere. The highest reductions were observed in slices packaged in 40% CO2/60% N2 after 60 days of storage at 4 °C.

10.
Int J Syst Evol Microbiol ; 70(12): 6106-6114, 2020 Dec.
Article in English | MEDLINE | ID: mdl-33048040

ABSTRACT

A novel cold-tolerant bacterium, designated strain YJ56T, was isolated from Antarctic soil collected from the Cape Burk area. Phylogenetic analysis through 16S rRNA gene sequence similarity revealed that strain YJ56T was most closely related to the genus Pseudarthrobacter, including Pseudarthrobacter oxydans DSM 20119T (99.06 % similarity), Pseudarthrobacter polychromogenes DSM 20136T (98.98 %) and Pseudarthrobacter sulfonivorans ALLT (98.76 %). The genome size (5.2 Mbp) of strain YJ56T was the largest among all the published genomes of Pseudarthrobacter type strains (4.2-5.0 Mbp). The genomic G+C content of strain YJ56T (64.7 mol%) was found to be consistent with those of other Pseudarthrobacter strains (62.0-71.0 mol%). The average nucleotide identity and average amino acid identity values between strain YJ56T and P. sulfonivorans ALLT were estimated at 84.1 and 84.2 %, respectively. The digital DNA-DNA hybridization value between the two strains was calculated to be 28.0 %. This rod-shaped and obligate aerobic strain exhibited no swimming or swarming motility. It had catalase activity but no oxidase activity. Cells grew at 4-28 °C (optimum, 13 °C) and pH 5.0-11.0 (optimum, pH 7.0) and with 0-6.0 % (w/v) NaCl (optimum, 0%) in Reasoner's 2A medium. MK-9 (H2) was the sole menaquinone. Two-dimensional TLC results revealed that the primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two glycolipids and phosphatidylinositol. Fatty acid methyl ester analysis showed that anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0 were the major cellular fatty acids in strain YJ56T. Based on phenotypic and genotypic characteristics, strain YJ56T represents a novel species of the genus Pseudarthrobacter, and thus the name Pseudarthrobacter psychrotolerans sp. nov is proposed. The type strain is YJ56T (=JCM 33881T=KACC 21510T).


Subject(s)
Micrococcaceae/classification , Phylogeny , Soil Microbiology , Antarctic Regions , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Glycolipids/chemistry , Micrococcaceae/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives
11.
Int J Syst Evol Microbiol ; 70(5): 3027-3036, 2020 May.
Article in English | MEDLINE | ID: mdl-32223834

ABSTRACT

A pink-coloured bacterium (strain KR32T) was isolated from cheese and assigned to the 'Arthrobacter agilis group'. Members of the 'pink Arthrobacter agilis group' form a stable clade (100 % bootstrap value) and contain the species Arthrobacter agilis, Arthrobacter ruber and Arthrobacter echini, which share ≥99.0 % 16S rRNA gene sequence similarity. Isolate KR32T showed highest 16S rRNA gene sequence similarity (99.9 %) to A. agilis DSM 20550T. Additional multilocus sequence comparison confirmed the assignment of strain KR32T to the clade 'pink A. agilis group'. Average nucleotide identity and digital DNA-DNA hybridization values between isolate KR32T and A. agilis DSM 20550T were 82.85 and 26.30 %, respectively. The G+C content of the genomic DNA of isolate KR32T was 69.14 mol%. Chemotaxonomic analysis determined anteiso-C15 : 0 as the predominant fatty acid and MK-9(H2) as the predominant menaquinone. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and monoacyldimannosyl-monoacylglycerol. The peptidoglycan type of the isolate was A3α. The carotenoid bacterioruberin was detected as the major pigment. At 10 °C, strain KR32T grew with increased concentrations of bacterioruberin and production of unsaturated fatty acids. Strain KR32T was a Gram-stain-positive, catalase-positive, oxidase-positive and coccus-shaped bacterium with optimal growth at 27-30 °C and pH 8. The results of phylogenetic and phenotypic analyses enabled the differentiation of the isolate from other closely related species of the 'pink A. agilis group'. Therefore, strain KR32T represents a novel species for which the name Arthrobacter bussei sp. nov. is proposed. The type strain is KR32T (=DSM 109896T=LMG 31480T=NCCB 100733T).


Subject(s)
Arthrobacter/classification , Cheese/microbiology , Food Microbiology , Phylogeny , Animals , Arthrobacter/isolation & purification , Bacterial Typing Techniques , Base Composition , Cattle , Cell Wall/chemistry , DNA, Bacterial/genetics , Fatty Acids/chemistry , Female , Germany , Glycolipids/chemistry , Milk , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , Pigmentation , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
12.
Int J Syst Evol Microbiol ; 69(9): 2862-2869, 2019 Sep.
Article in English | MEDLINE | ID: mdl-31274399

ABSTRACT

Four Gram-stain positive, rod-shaped bacterial isolates, strains JZ R-183T, JZ RK-117, DI-46 and JZ R-35T, were recovered from bulk tank raw cow's milk from three different dairy farms in Germany. Analysis of their 16S rRNA gene sequences indicated that these isolates belonged to the family Micrococcaceae, closely related to the genera Arthrobacter, Neomicrococcus,Glutamicibacter and Citricoccus. The 16S rRNA gene sequence similarity between the isolates and the next related type strains was below 97.3 %. Phylogenetic analysis of 16S rRNA, recA and gyrB genes revealed that these isolates formed two different groups in an independent cluster within the family Micrococcaceae. Chemotaxonomic analyses determined anteiso-C15 : 0 as predominant fatty acid, but also large amounts of iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 were detected. The menaquinones MK-9(H2) and MK-7(H2) were present in all of the isolates and the polar lipid pattern contained the phospholipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol and a glycolipid. The peptidoglycan type of the isolates was A4α, with alanine, lysine and glutamate as dominating cell wall amino acids. The fatty acid and menaquinone profile differentiated the strains from the genera Arthrobacter, Neomicrococcus,Citricoccus and Glutamicibacter. The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that the isolates belonged to two novel species of a novel genus, for which the names Galactobacter caseinivorans gen. nov., sp. nov. and Galactobacter valiniphilus sp. nov. are proposed. The type strains are JZ R-183T (=DSM 107700T=LMG 30902T) and JZ R-35T (=DSM 107699T=LMG 30901T).


Subject(s)
Micrococcaceae/classification , Milk/microbiology , Phylogeny , Animals , Bacterial Load , Bacterial Typing Techniques , Base Composition , Cattle/microbiology , Cell Wall/chemistry , DNA, Bacterial/genetics , Fatty Acids/chemistry , Female , Germany , Glycolipids/chemistry , Micrococcaceae/isolation & purification , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
13.
Int J Syst Evol Microbiol ; 69(6): 1767-1774, 2019 Jun.
Article in English | MEDLINE | ID: mdl-30990394

ABSTRACT

A Gram-reaction-positive, non-spore-forming, rod-shaped bacterium, strain C1-50T, was isolated from a natural cave in Jeju, Republic of Korea by using the serial dilution plating method. Results of phylogenetic analysis using 16S rRNA gene sequences showed that strain C1-50T belonged to the family Micrococcaceae but had the highest sequence similarity to Arthrobacter halodurans JSM 078085T (96.18 %) and Arthrobacter globiformis DSM 20124T (96.04 %). The 16S rRNA gene sequence similarities between strain C1-50T and other members of the family were lower than 96.0 %. The cell-wall peptidoglycan type was A3α with an l-Lys-l-Ala2. Whole-cell sugars consisted largely of glucose and galactose. The predominant menaquinone was MK-9(H2) with smaller components of MK-7(H2) and MK-8(H2). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The cellular fatty acids consisted of saturated, unsaturated, anteiso-branched and iso-branched components. The G+C content of genomic DNA was 68.8 mol% (draft genome sequence). On the basis of morphological and chemotaxonomic differences and distinct phylogenetic clustering, it was concluded that the organism represents a novel species of a new genus in the family Micrococcaceae, for which the name Specibacter cremeus gen. nov., sp. nov. is proposed. The type strain is C1-50T (=KCTC 39557T=DSM 100066T).


Subject(s)
Caves/microbiology , Micrococcaceae/classification , Phylogeny , Bacterial Typing Techniques , Base Composition , Cell Wall/chemistry , DNA, Bacterial/genetics , Fatty Acids/chemistry , Glycolipids/chemistry , Micrococcaceae/isolation & purification , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
14.
Food Res Int ; 106: 363-373, 2018 04.
Article in English | MEDLINE | ID: mdl-29579936

ABSTRACT

Italian salami were sonicated in different times (0, 3, 6 and 9min) using ultrasound bath (US, 25kHz). The effect of sonication on microbial growth (lactic acid bacteria and Micrococcaceae), lipid and protein oxidation, total heme pigments (THP), non heme iron (NHI) and metmyoglobin (MMb) was investigated during processing (0, 2, 15, and 28days) and storage (1, 30, and 120days). US enhanced growth of microorganisms (P<0.05), mainly for the treatment 9min of sonication. The lipid (peroxide value and TBARS) and protein (thiol group) oxidative reactions were accelerated by US (P<0.05) and they should be considered to maintain Italian salami quality. Sonication contributed to maintenance of THP (P<0.05), especially during storage. MMb pigment was not affected by sonication (P>0.05). This study presented some features of US application that could be explored in the manufacture of Italian salami.


Subject(s)
Chemical Phenomena/radiation effects , Food Microbiology , Meat Products/radiation effects , Sonication , Fermentation , Food Handling/methods , Heme/analysis , Heme/radiation effects , Iron/analysis , Iron/radiation effects , Italy , Lactobacillales/growth & development , Lactobacillales/radiation effects , Lipid Peroxidation/radiation effects , Meat Products/analysis , Meat Products/microbiology , Metmyoglobin/analysis , Metmyoglobin/radiation effects , Micrococcaceae/growth & development , Micrococcaceae/radiation effects , Oxidation-Reduction/radiation effects , Proteins/chemistry , Proteins/radiation effects , Thiobarbituric Acid Reactive Substances/analysis
15.
Int J Food Microbiol ; 251: 33-40, 2017 Jun 19.
Article in English | MEDLINE | ID: mdl-28384620

ABSTRACT

The rationale of the present study was to evaluate the potential of microbial adjunct cultures including Kocuria varians and/or Yarrowia lipolytica strains in the recovery of the typical sensory profile of traditional (raw-milk) Tetilla cheese. Four batches of Tetilla cheese, a short ripened cows' milk cheese produced in Galicia (NW Spain), were made in duplicate from pasteurized milk inoculated with different microbial cultures. A control batch was manufactured by adding a mesophilic commercial D-starter only. The other three batches were made with the same starter after a cheese-milk pre-ripening step carried out with (i) an adjunct culture of K. varians, (ii) an adjunct culture of Y. lipolytica, or (iii) a combination of both adjunct cultures. The highest pH and water activity values, associated with softer textures were determined in the cheeses manufactured with the Y. lipolytica adjunct after 21days of ripening. The contents of the volatile compounds 3-methylbutanol, dimethyl disulfide and dimethyl trisulfide were higher in the cheeses made with only the K. varians adjunct than in the cheeses made with the only yeast adjunct and in the control cheeses. The contents of hexanoic and octanoic acids were highest in the cheeses made with the Y. lipolytica adjunct, and levels of ethyl hexanoate, ethyl octanoate and ethyl decanoate were higher in the cheeses made with only the yeast adjunct than in the other batches of cheese. The cheeses manufactured with both adjunct cultures were awarded the highest scores for flavour and overall sensory parameters (considering the standards of the traditional product) and were considered very similar to 'good quality' artisanal raw-milk cheeses. We conclude that use of selected Micrococcaceae and Y. lipolytica strains as adjunct cultures would differentiate the sensory properties and contribute to the quality and typicality of the short-ripened rennet-curd Galician Tetilla and Arzúa-Ulloa cheeses.


Subject(s)
Cheese/microbiology , Flavoring Agents/chemistry , Micrococcaceae/metabolism , Milk/microbiology , Yarrowia/metabolism , Animals , Caproates/metabolism , Caprylates/metabolism , Cattle , Cheese/analysis , Decanoates/metabolism , Fermentation , Flavoring Agents/analysis , Food Microbiology , Milk/chemistry , Spain , Taste
16.
Cureus ; 8(8): e731, 2016 Aug 10.
Article in English | MEDLINE | ID: mdl-27630804

ABSTRACT

Recently there have been reports of gram-positive cocci which are morphologically similar to both Staphylococci and the Micrococci. These bacteria have been identified as Kocuria species with the help of automated identification system and other molecular methods including 16S rRNA (ribosomal ribonucleic acid) evaluation. Kocuria belongs to the family Micrococcaceae which also includes Staphylococcus species and Micrococcus species. Isolation and clinical significance of these bacteria from human specimens warrant great caution as it does not necessarily confirm infection due to their ubiquitous presence, and as a normal flora of skin and mucous membranes in human and animals. Most clinical microbiology laboratories ignore such bacteria as laboratory and specimen contaminants. With increasing reports of infections associated with these bacteria, it is now important for clinical microbiologists to identify and enumerate the virulence and antibiotic susceptibility patterns of such bacteria and assist clinicians in improving the patient care and management. We review the occurrence and clinical significance of Kocuria species.

17.
Article in English | WPRIM (Western Pacific) | ID: wpr-228226

ABSTRACT

Contamination with sanitary microorganisms from Enterobacteriaceae, Pseudomonadaceae, Staphylococcaceae, Micrococcaceae and Bacillaceae families in flower bee pollen from Bulgaria after one-year vacuum-packed cold storage has been found. Dried flower bee pollens intended for human consumption were with high incidence rate of contamination with Pantoea sp. (P. agglomerans and P. agglomerans bgp6) (100%), Citrobacter freundii (47%), Proteus mirabilis (31.6%), Serratia odorifera (15.8%) and Proteus vulgaris (5.3%). Bee pollens were also positive for the culture of microorganisms from Staphylococcaceae, Micrococcaceae and Bacillaceae families: Staphylococcus hominis subsp hominis, Staphylococcus epidermidis, Arthrobacter globiformis, Bacillus pumilis, Bacillus subtilis and Bacillus amyloliquefaciens. It was concluded that, if consumed directly, the vacuum-packed cold stored dried bee pollen, harvested according hygienic requirements from bee hives in industrial pollution-free areas without intensive crop production, is not problem for healthy human.


Subject(s)
Humans , Arthrobacter , Bacillaceae , Bacillus , Bacillus subtilis , Bees , Bulgaria , Citrobacter freundii , Crop Production , Enterobacteriaceae , Flowers , Incidence , Micrococcaceae , Pantoea , Pollen , Proteus mirabilis , Proteus vulgaris , Pseudomonadaceae , Serratia , Staphylococcaceae , Staphylococcus epidermidis , Staphylococcus hominis , Urticaria , Vacuum
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