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Frontiers in Microbiology 2019is an ethnic, naturally fermented soybean product consumed in the Sikkim Himalayan region of India. In the present study, the whole metagenome sequencing approach was...
is an ethnic, naturally fermented soybean product consumed in the Sikkim Himalayan region of India. In the present study, the whole metagenome sequencing approach was adopted to examine the microbial diversity and related functional potential of , consumed in different seasons. Firmicutes was the abundant phylum in , ranging from 82.31 to 93.99% in different seasons, followed by Actinobacteria and Proteobacteria. At the species level, the prevalent microorganisms were , , , , , and . The abundance of microbial species varied significantly in different seasons. Further, the genomic presence of some undesirable microbes like , , , and , were also detected in the specific season. The metagenomic analysis also revealed the existence of bacteriophages belonging to the family , , and . Examination of the metabolic potential of the metagenome depicted information about the biocatalysts, presumably involved in the transformation of protein and carbohydrate polymers into bioactive molecules of health-beneficial effects. The genomic resource of several desirable enzymes was identified, such as β-galactosidase, β-glucosidase, β-xylosidase, and glutamate decarboxylase, etc. The catalytic function of a novel glutamate decarboxylase gene was validated for the biosynthesis of γ-aminobutyric acid (GABA). The results of the present study highlight the microbial and genomic resources associated with , and its importance in functional food industry.
PubMed: 31428064
DOI: 10.3389/fmicb.2019.01744 -
Heliyon Dec 2018The objective of the present work was to examine the bacterial flora associated with the oral cavity of Indian cobra and to study their antibiogram.
OBJECTIVES
The objective of the present work was to examine the bacterial flora associated with the oral cavity of Indian cobra and to study their antibiogram.
METHODS
Oral swabs, collected from six healthy (4 males and 2 females) adult cobra, were subjected to microbiological examination through differential media. A total of 74 isolates which demonstrated noticeable colony characters were studied with different biochemical tests. The strains that showed distinctive colonies, morphology and biochemical parameters were additionally subjected to phylogenetic characterization using 16S rRNA gene sequences. Further, the isolates were subjected to antimicrobial susceptibility testing using ICOSA-20-plus and ICOSA-20-minus.
RESULTS
Microscopic examination of the oral cavity of Indian cobra revealed the dominance of Gram-negative bacteria over Gram-positive. The oral microflora constituted of bacteria such as sp. ( A); sp. (); sp. (); ; sp.; sp. (); sp. () sp. (); sp. (); sp.; sp.; sp. ( and ); sp. (); sp. (); sp.; sp. and sp. Most of the isolates were resistant towards antibiotics such as Penicillin, Cefpodoxime, Amoxyclav, Co-Trimoxazole, Ticarcillin, Erythromycin and Nalidixic acid while sensitive towards Ciprofloxacin, Gentamicin, Ofloxacin, Sparfloxacin, Tobromycin, Ceftriaxone, Tetracycline, Novobiocin and Imipenem.
CONCLUSIONS
The secondary complications of the snake bite victims should be managed with appropriate antibiotics after proper examination of the bacterial flora from the wound sites.
PubMed: 30582036
DOI: 10.1016/j.heliyon.2018.e01008 -
International Journal of Molecular... Feb 2018The new type of core oligosaccharide in 40A and 41 lipopolysaccharides has been investigated by ¹H and C NMR spectroscopy, electrospray ionization mass spectrometry...
The new type of core oligosaccharide in 40A and 41 lipopolysaccharides has been investigated by ¹H and C NMR spectroscopy, electrospray ionization mass spectrometry and chemical methods. Core oligosaccharides of both strains were chosen for structural analysis based on the reactivity of LPSs with serum against 40A core oligosaccharide-diphtheria toxoid conjugate. Structural analyses revealed that 40A and 41 LPSs possess an identical core oligosaccharide.
Topics: Antigens, Bacterial; Immune Sera; Lipopolysaccharides; Magnetic Resonance Spectroscopy; Molecular Structure; Oligosaccharides; Proteus penneri; Spectrometry, Mass, Electrospray Ionization; Structure-Activity Relationship
PubMed: 29495556
DOI: 10.3390/ijms19030676 -
Antimicrobial Agents and Chemotherapy May 2018The complete nucleotide sequences of six IMP-4-encoding plasmids recovered from isolates of wildlife origin were characterized. Sequencing data showed that plasmids of...
Characterization of the Complete Nucleotide Sequences of IMP-4-Encoding Plasmids, Belonging to Diverse Inc Families, Recovered from Enterobacteriaceae Isolates of Wildlife Origin.
The complete nucleotide sequences of six IMP-4-encoding plasmids recovered from isolates of wildlife origin were characterized. Sequencing data showed that plasmids of different incompatibility groups (IncM, IncI1, IncF, and nontypeable [including an IncX5_2 and two pPrY2001-like]) carried the -carrying integrons In809 or In1460. Most of the plasmids carried an (A) region, and -like, , and genes. Finally, plasmid analysis revealed the involvement of two different IS- and Tn-associated mechanisms in the mobilization of IMP-4-encoding integrons.
Topics: Anti-Bacterial Agents; Enterobacteriaceae; Enterobacteriaceae Infections; Gene Transfer, Horizontal; Plasmids
PubMed: 29483121
DOI: 10.1128/AAC.02434-17 -
International Journal of Systematic and... Feb 2018A Gram-negative, facultatively anaerobic bacillus, strain 08MAS2615, was isolated from the flesh of a pigeon specimen collected in Ma'anshan, Anhui province, China....
A Gram-negative, facultatively anaerobic bacillus, strain 08MAS2615, was isolated from the flesh of a pigeon specimen collected in Ma'anshan, Anhui province, China. Phylogenetic analysis of 16S rRNA gene sequences confirmed that strain 08MAS2615 belonged to the genus Proteus, and formed an independent branch which was clearly separated from the other six known species of Proteus. Strain 08MAS2615 was more closely related to Proteus vulgaris ATCC 29905 and Proteus penneri NCTC 12737 than other Proteus species. Similar independent phylogenetic results were obtained using rpoB gene sequence analysis, whereas strain 08MAS2615 clustered near the species of Proteus cibarius JS9 and Proteus terrae N5/687. Furthermore, the genome-wide core-single nucleotide polymorphism-based phylogenetic tree confirmed that strain 08MAS2615 formed a monophyletic and robust clade. Based on whole-genome sequences, the range of in silico DNA-DNA hybridization and average nucleotide identity between strain 08MAS2615 and the six Proteus species were 25.5-48.8 % and 82.8-92.9 %, respectively, less than the proposed cutoff level for species delineation, i.e. 70 and 95 %. In addition, the major cellular fatty acid profile of strain 08MAS2615 was C14 : 0 (12.4 %), C16 : 0 (23.8 %), C17 : 0cyclo (14.4 %), summed feature 2 (C16 : 1iso I/C14 : 0 3-OH) (11.0 %), summed feature 3 (C16 : 1ω7c/16 : 1ω6c) (18.5 %) and summed feature 8 (C18 : 1ω6c) (18.6 %). On the basis of these results, strain 08MAS2615 represents a novel species of the genus Proteus, for which the name Proteuscolumbae sp. nov. is proposed with strain 08MAS2615 (=DSM 104686=CGMCC 1.15982) designated as the species type strain.
Topics: Animals; Bacterial Typing Techniques; Base Composition; China; Columbidae; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Phylogeny; Proteus; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29297845
DOI: 10.1099/ijsem.0.002541 -
Zhongguo Zhong Yao Za Zhi = Zhongguo... Nov 2017To investigate the microbial contamination in Chinese herbal decoction pieces with different functional types by studying the total aerobic microbial count (TAMC), and...
To investigate the microbial contamination in Chinese herbal decoction pieces with different functional types by studying the total aerobic microbial count (TAMC), and total yeast and mould count (TYMC) in 40 samples of 8 types of root decoction pieces; further evaluate the contamination load of bile-resistant Gram-negative bacteria, and identify the Gram-negative bacteria by using biochemical identification system for Gram-negative bacteria. Our results showed that the TAMC value was more than 1 000 CFU•g⁻¹ in 85% (34/40) samples, and was more than 100 CFU•g⁻¹ in 30% (12/40) samples; the contamination of bile-resistant Gram-negative bacteria was detected in 45% (18/40) of the samples. The bile-resistant Gram-negative bacteria load of seven batches of samples was N>1 000 MPN•g⁻¹. Sixteen bacterium strains including Serratia plymouthensis, Cedecea neteri, Escherichia vulneris, Klebsiella oxytoca, Enterobacter amnigenus, E. cloacae, E. sakazakii, Proteus penneri and E. gergoviae were obtained and identified. E. cloacae was the predominant bacterium that was isolated from Salviae Miltiorrhizae Radix et Rhizoma, while E. amnigenus, Yersinia pseudotuberculosis was the typical bacterium of Ophiopogonis Radix and Codonopsis Radix, respectively. All these suggested that the contamination of bile-resistant Gram-negative bacteria was severe for the root decoction pieces in Wuhan city. Microbial species have certain selection specificity for medicinal ingredients, so the type and limit of control bacteria for detection should be formulated according to the pollution type and quantity of bile-resistant Gram-negative bacteria.
Topics: Anti-Bacterial Agents; Bile; Drugs, Chinese Herbal; Gram-Negative Bacteria; Plant Roots
PubMed: 29271151
DOI: 10.19540/j.cnki.cjcmm.20171017.001 -
Annals of Medical and Health Sciences... 2016species cause a variety of community- and hospital-acquired illnesses. Synthesis of β-lactamases is the predominant mechanism for resistance to β-lactam antibiotics....
BACKGROUND
species cause a variety of community- and hospital-acquired illnesses. Synthesis of β-lactamases is the predominant mechanism for resistance to β-lactam antibiotics. Among the β-lactamases, extended spectrum β-lactamases (ESBLs) and AmpC β-lactamases are the most common.
AIM
The objective of this study was to determine the occurrence of ESBL and AmpC β-lactamases in species among various clinical isolates at a tertiary care hospital, India.
MATERIALS AND METHODS
This study was done to identify various species of from clinical samples ( = 3922). Antimicrobial susceptibility was performed by Kirby-Bauer disc diffusion method. ESBL production was detected by modified double-disc synergy test and indirect modified three-dimensional tests and AmpC β-lactamase production by AmpC disc test and modified Hodge test.
RESULTS
species were isolated in 5.4% (101/1876) specimens. Three species isolated were 62.4% (63/101), 29.7% (30/101), and 7.9% (8/101). ESBL producers confirmed by both tests were of 88.1% (89/101). Only AmpC β-lactamase was produced by four isolates. Coproduction of ESBL and AmpC β-lactamase was observed in 58.4% (52/89) of isolates. Twelve isolates were non-β-lactamase producers. Multidrug resistance (MDR) was found in 95.1% (96/101) of isolates, 50.5% (51/101) were possibly extensively drug resistant and none were pan drug resistant. None of the isolates were resistant to piperacillin-tazobactam. isolates exhibited high resistance to most of the antibiotics.
CONCLUSIONS
A high prevalence of ESBL and AmpC β-lactamases was found that concurrently showed MDR. Phenotypic methods for the detection of β-lactamases are easy and simple and can be implemented in routine diagnostic laboratories along with susceptibility testing. These data will assist the clinicians in the management and control of infections.
PubMed: 28503342
DOI: 10.4103/amhsr.amhsr_413_15 -
Medical Microbiology and Immunology Dec 2016The frequency of P. penneri isolation from hospital patients, mostly from urine and wounds, keeps on growing, and numerous isolates are multi-drug resistant. P. penneri...
The frequency of P. penneri isolation from hospital patients, mostly from urine and wounds, keeps on growing, and numerous isolates are multi-drug resistant. P. penneri rods produce lipopolysaccharide (LPS), which may lead to the septic shock. Until now, O-specific polysaccharide has been the best structurally and serologically characterized region of P. penneri LPS. It is worth having an insight into the serological specificity of both poly- and oligosaccharide parts of P. penneri LPS. The P. penneri core region is less structurally diverse than OPS, but still, among other enterobacterial LPS core regions, it is characterized by structural variability. In the present study, the serological reactivity of 25 P. penneri LPS core regions was analyzed by ELISA, passive immunohemolysis and Western blot technique using five polyclonal P. penneri antisera after or without their adsorption with the respective LPSs. The results allowed the assignment of the tested strains to five new core serotypes, which together with published serological studies led to the creation of the first serotyping scheme based on LPS core reactivities of 35 P. penneri and three P. mirabilis strains. Together with the O types scheme, it will facilitate assigning Proteus LPSs of clinical isolates into appropriate O and R serotypes.
Topics: Animals; Epitopes; Immune Sera; Lipopolysaccharides; Proteus penneri; Rabbits; Serogroup; Serotyping; Virulence Factors
PubMed: 27469376
DOI: 10.1007/s00430-016-0468-8 -
Microbial Ecology Nov 2016Proteus spp. bacteria were first described in 1885 by Gustav Hauser, who had revealed their feature of intensive swarming growth. Currently, the genus is divided into... (Review)
Review
Proteus spp. bacteria were first described in 1885 by Gustav Hauser, who had revealed their feature of intensive swarming growth. Currently, the genus is divided into Proteus mirabilis, Proteus vulgaris, Proteus penneri, Proteus hauseri, and three unnamed genomospecies 4, 5, and 6 and consists of 80 O-antigenic serogroups. The bacteria are known to be human opportunistic pathogens, isolated from urine, wounds, and other clinical sources. It is postulated that intestines are a reservoir of these proteolytic organisms. Many wild and domestic animals may be hosts of Proteus spp. bacteria, which are commonly known to play a role of parasites or commensals. However, interesting examples of their symbiotic relationships with higher organisms have also been described. Proteus spp. bacteria present in soil or water habitats are often regarded as indicators of fecal pollution, posing a threat of poisoning when the contaminated water or seafood is consumed. The health risk may also be connected with drug-resistant strains sourcing from intestines. Positive aspects of the bacteria presence in water and soil are connected with exceptional features displayed by autochthonic Proteus spp. strains detected in these environments. These rods acquire various metabolic abilities allowing their adaptation to different environmental conditions, such as high concentrations of heavy metals or toxic substances, which may be exploited as sources of energy and nutrition by the bacteria. The Proteus spp. abilities to tolerate or utilize polluting compounds as well as promote plant growth provide a possibility of employing these microorganisms in bioremediation and environmental protection.
Topics: Animals; Environment; Gastrointestinal Microbiome; Houseflies; Humans; Insect Vectors; Proteus; Proteus Infections; Soil Microbiology; Virulence Factors; Water Microbiology; Water Pollution
PubMed: 26748500
DOI: 10.1007/s00248-015-0720-6 -
Journal of Food Science and Technology Jan 2016Histamine formation and bacteriological changes caused by temperature abuse commonly occurring in the manufacturing process of standard canned tuna was assessed in...
Histamine formation and bacteriological changes caused by temperature abuse commonly occurring in the manufacturing process of standard canned tuna was assessed in microbiologically challenged tonggol (Thunnus tonggol). The in situ challenge was performed by water-soaking at 26-28 °C for 7 h to ensure the multiplication and active phase of fish microflora. Right after pre-cooking to back-bone temperature (BBT) of 50-52 °C, histamine dropped to 5.17 ± 2.71 ppm, and slowly reached 6.84 ± 1.69 ppm at 16 h abuse. On the contrary, histamine was reduced to 2.87 ± 1.23 ppm and eventually reached 5.01 ± 1.32 ppm at 24 h abuse in the pre-cooked fish previously frozen. The numbers of total aerobic bacteria, Enterobactericeae, psychrotroph, histamine forming bacteria (HFB) and diversity of fish microflora were revealed by cultural and nested PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) techniques. Interestingly, frozen storage effectively halted histamine formation in raw fish throughout 16 h abuse despite the presence of HFB. These included the prolific strains of Morganella morganii, Proteus penneri, Proteus mirabilin, Citrobacter spp. The nested PCR-DGGE profile confirmed the presence of M. morganii and Citrobacter spp. in raw fish. These prolific strains were hardly observed in the precooked fish previously frozen. Frozen storage did not only promote even histamine distribution throughout fish muscle but also enhanced histamine loss during thawing and pre-cooking. Therefore, pre-cooking and frozen storage were proven to be the effective combined hurdles not only to reduce but also prolong histamine formation of the challenged toggol throughout 24 h of temperature abuse during canning process.
PubMed: 26787946
DOI: 10.1007/s13197-015-2042-6