Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases

AbstractIn the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin–Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o-Nitrophenyl-β-d-galactopyranoside (ONPG) and p-Nitrophenyl-β-d-fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.

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Characterization of the β-lactamase specified by the resistance factor R-1818 in Escherichia coli K12 and other Gram-negative bacteria

Biochemical Journal ◽

10.1042/bj1230501 ◽

1971 ◽

Vol 123 (4) ◽

pp. 501-505 ◽

Cited By ~ 13

Author(s):

J. W. Dale

Keyword(s):

Escherichia Coli ◽

Host Species ◽

Host Bacterium ◽

Gram Negative Bacteria ◽

Gram Negative ◽

E Coli ◽

R Factor ◽

Relationship Of ◽

The Relationship

1. The amino acid composition of the β-lactamase from E. coli (R-1818) was determined. 2. The R-1818 β-lactamase is inhibited by formaldehyde, hydroxylamine, sodium azide, iodoacetamide, iodine and sodium chloride. 3. The Km values for benzylpenicillin, ampicillin and oxacillin have been determined by using the R-factor enzyme from different host species. The same values were obtained, irrespective of the host bacterium. 4. The molecular weight of the enzyme was found to be 44600, and was the same for all host species. 5. The relationship of R-1818 and R-GN238 β-lactamases is discussed.

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Myeloperoxidase Selectively Binds and Selectively Kills Microbes

Infection and Immunity ◽

10.1128/iai.00910-09 ◽

2010 ◽

Vol 79 (1) ◽

pp. 474-485 ◽

Cited By ~ 33

Author(s):

Robert C. Allen ◽

Jackson T. Stephens

Keyword(s):

Streptococcus Pyogenes ◽

Direct Evidence ◽

Minimal Bactericidal Concentration ◽

Viridans Streptococci ◽

E Coli ◽

Horse Blood ◽

Valid Comparison ◽

Relationship Of ◽

The Relationship ◽

Lysed Horse Blood

ABSTRACTMyeloperoxidase (MPO) is reported to selectively bind to bacteria. The present study provides direct evidence of MPO binding selectivity and tests the relationship of selective binding to selective killing. The microbicidal effectiveness of H2O2and of OCl−was compared to that of MPO plus H2O2. Synergistic microbicidal action was investigated by combiningStreptococcus sanguinis, a H2O2-producing microbe showing low MPO binding, with high-MPO-bindingEscherichia coli,Staphylococcus aureus, orPseudomonas aeruginosawithout exogenous H2O2, with and without MPO, and with and without erythrocytes (red blood cells [RBCs]). Selectivity of MPO microbicidal action was conventionally measured as the MPO MIC and minimal bactericidal concentration (MBC) for 82 bacteria includingE. coli,P. aeruginosa,S. aureus,Enterococcus faecalis,Streptococcus pyogenes,Streptococcus agalactiae, and viridans streptococci. Both H2O2and OCl−destroyed RBCs at submicrobicidal concentrations. Nanomolar concentrations of MPO increased H2O2microbicidal action 1,000-fold. Streptococci plus MPO produced potent synergistic microbicidal action against all microbes tested, and RBCs caused only a small decrease in potency without erythrocyte damage. MPO directly killed H2O2-producingS. pyogenesbut was ineffective against non-H2O2-producingE. faecalis. The MPO MICs and MBCs forE. coli,P. aeruginosa, andS. aureuswere significantly lower than those forE. faecalis.The streptococcal studies showed much higher MIC/MBC results, but such testing required lysed horse blood-supplemented medium, thus preventing valid comparison of these results to those for the other microbes.E. faecalisMPO binding is reportedly weak compared to binding ofE. coli,P. aeruginosa, andS. aureusbut strong compared to binding of streptococci. Selective MPO binding results in selective killing.

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A comparison of the levels of faecal indicator bacteria in water and human faeces in a rural area of a tropical developing country (Sierra Leone)

Journal of Hygiene ◽

10.1017/s0022172400070558 ◽

1982 ◽

Vol 89 (1) ◽

pp. 69-78 ◽

Cited By ~ 21

Author(s):

R. C. Wright

Keyword(s):

Sierra Leone ◽

Water Sources ◽

Indicator Bacteria ◽

Rural Settlements ◽

Faecal Coliforms ◽

Human Faeces ◽

E Coli ◽

Faecal Samples ◽

Relationship Of ◽

The Relationship

SUMMARYThe levels of faecal coliforms (FC), indole-positive FC (presumptiveEscherichia coli), faecal streptococci (FS),Streptococcus faecalisandClostridium perfringensin the natural water sources used by 29 rural settlements in Sierra Leone were investigated. Levels of the same indicators in human faeces were also investigated. The incidence ofSalmonellaspp. in both habitats and the temperature, pH and conductivity of water sources were also recorded. All water sources were contaminated with the indicator bacteria, mean numbers of which occurred in the relationship FC > presumptiveE. coli≏ FS ≏C. perfringens>S. faecalis.FC were also predominant in human faeces, the relationship of means being FC ≏ presumptiveE. coli> FS >S. faecalis>C. perfringens.The need for confirmation of FC counts obtained from water sources was indicated by the large number of positive tubes produced in the FC multiple-tube dilution test from some samples which could not be confirmed as presumptiveE. coli. Salmonellaspp. were isolated from 13 water sources and 6% of faecal samples. Mean water temperature was high (26·2 °C), pH low (5·04) and conductivity low (34μS cm−1). PresumptiveE. coliwas considered the most appropriate indicator of faecal pollution of the types of water investigated.

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Purification and properties of a germination-specific cortex-lytic enzyme from spores of Bacillus megaterium KM

Biochemical Journal ◽

10.1042/bj2420573 ◽

1987 ◽

Vol 242 (2) ◽

pp. 573-579 ◽

Cited By ~ 40

Author(s):

S J Foster ◽

K Johnstone

Keyword(s):

Bacillus Megaterium ◽

Maximal Activity ◽

Lytic Enzyme ◽

Bacillus Species ◽

Muramic Acid ◽

Specific Enzyme ◽

Purification And Properties ◽

Proposed Model ◽

Relationship Of ◽

The Relationship

Two peptidoglycan-lytic enzyme activities were isolated from spores of Bacillus megaterium KM. Surface-bound lytic enzyme was extracted from dormant spores and hydrolysed a variety of peptidoglycan substrates including isolated spore cortex, but did not cause refractility changes in permeabilized spores. Germination-specific lytic enzyme activity appeared early in germination and had minimal activity on isolated peptidoglycan substrates, but caused refractility changes in permeabilized spores of several Bacillus isolated peptidoglycan substrates, but caused refractility changes in permeabilized spores of several Bacillus species. The germination-specific lytic enzyme was shown to be a heat-sensitive 29 kDa protein with maximal activity at pH 6.5. It catalysed post-commitment muramic acid delta-lactam synthesis and displayed an inhibitor profile similar to that for post-commitment A600 loss. The relationship of the germination-specific enzyme to a recently proposed model of spore germination is discussed.

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CHEMICAL STUDIES ON HOST-VIRUS INTERACTIONS

Journal of Experimental Medicine ◽

10.1084/jem.84.5.511 ◽

1946 ◽

Vol 84 (5) ◽

pp. 511-523 ◽

Cited By ~ 42

Author(s):

Seymour S. Cohen ◽

Thomas F. Anderson

Keyword(s):

Respiratory Rate ◽

Cytoplasmic Granules ◽

E Coli ◽

T4 Bacteriophage ◽

Chemical Studies ◽

Host Virus Interactions ◽

Virus Interactions ◽

Relationship Of ◽

The Relationship ◽

Similar Substance

The addition of active or irradiated T2 bacteriophage and T4 bacteriophage to E. coli B stops bacterial multiplication. The respiratory rate and respiratory quotient of the inhibited bacteria remained at the values observed just before infection. A respiratory rate decrease which occasionally appears can be roughly correlated with change of turbidity of the suspension. An intracellular inhibitor of multiplication appears to be liberated into lysates. A similar substance has been separated from normal E. coli B after sonic disintegration. These bacteriostatic preparations contain cytoplasmic granules with lactic acid dehydrogenase activity. The relationship of these phenomena to the interference effect in this system and others has been considered.

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Genetic Characterization of Escherichia coli Populations from Host Sources of Fecal Pollution by Using DNA Fingerprinting

Applied and Environmental Microbiology ◽

10.1128/aem.69.5.2587-2594.2003 ◽

2003 ◽

Vol 69 (5) ◽

pp. 2587-2594 ◽

Cited By ~ 81

Author(s):

Sandra L. McLellan ◽

Annette D. Daniels ◽

Alissa K. Salmore

Keyword(s):

Escherichia Coli ◽

Pairwise Comparison ◽

Fecal Pollution ◽

Host Animal ◽

Host Group ◽

E Coli ◽

Single Host ◽

Relationship Of ◽

The Relationship

ABSTRACT Escherichia coli isolates were obtained from common host sources of fecal pollution and characterized by using repetitive extragenic palindromic (REP) PCR fingerprinting. The genetic relationship of strains within each host group was assessed as was the relationship of strains among different host groups. Multiple isolates from a single host animal (gull, human, or dog) were found to be identical; however, in some of the animals, additional strains occurred at a lower frequency. REP PCR fingerprint patterns of isolates from sewage (n = 180), gulls (n = 133), and dairy cattle (n = 121) were diverse; within a host group, pairwise comparison similarity indices ranged from 98% to as low as 15%. A composite dendrogram of E. coli fingerprint patterns did not cluster the isolates into distinct host groups but rather produced numerous subclusters (approximately >80% similarity scores calculated with the cosine coefficient) that were nearly exclusive for a host group. Approximately 65% of the isolates analyzed were arranged into host-specific groups. Comparable results were obtained by using enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis (PFGE), where PFGE gave a higher differentiation of closely related strains than both PCR techniques. These results demonstrate that environmental studies with genetic comparisons to detect sources of E. coli contamination will require extensive isolation of strains to encompass E. coli strain diversity found in host sources of contamination. These findings will assist in the development of approaches to determine sources of fecal pollution, an effort important for protecting water resources and public health.

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A One Health Review of Community-Acquired Antimicrobial-Resistant Escherichia coli in India

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph182212089 ◽

2021 ◽

Vol 18 (22) ◽

pp. 12089

Author(s):

Keerthana Rajagopal ◽

Sujith J. Chandy ◽

Jay P. Graham

Keyword(s):

Escherichia Coli ◽

One Health ◽

Intestinal Bacteria ◽

One Dimension ◽

E Coli ◽

The One ◽

Relationship Of ◽

The Relationship ◽

Third Generation Cephalosporins ◽

Health Review

Antimicrobial resistance (AMR) threatens to undermine nearly a century of progress since the first use of antimicrobial compounds. There is an increasing recognition of the links between antimicrobial use and AMR in humans, animals, and the environment (i.e., One Health) and the spread of AMR between these domains and around the globe. This systematic review applies a One Health approach—including humans, animals, and the environment—to characterize AMR in Escherichia coli in India. E. coli is an ideal species because it is readily shared between humans and animals, its transmission can be tracked more easily than anaerobes, it can survive and grow outside of the host environment, and it can mobilize AMR genes more easily than other intestinal bacteria. This review synthesized evidence from 38 studies examining antimicrobial-resistant E. coli (AR-E) across India. Studies of AR-E came from 18 states, isolated from different sample sources: Humans (n = 7), animals (n = 7), the environment (n = 20), and combinations of these categories, defined as interdisciplinary (n = 4). Several studies measured the prevalence of AMR in relation to last-line antimicrobials, including carbapenems (n = 11), third-generation cephalosporins (n = 18), and colistin (n = 4). Most studies included only one dimension of the One Health framework, highlighting the need for more studies that aim to characterize the relationship of AMR across different reservoirs of E. coli.

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Ontology-Aware Deep Learning Enables Ultrafast, Accurate and Interpretable Source Tracking among Sub-Million Microbial Community Samples from Hundreds of Niches

10.1101/2020.11.01.364208 ◽

2020 ◽

Author(s):

Yuguo Zha ◽

Hui Chong ◽

Hao Qiu ◽

Kai Kang ◽

Yuzheng Dun ◽

...

Keyword(s):

Deep Learning ◽

Microbial Community ◽

Community Sample ◽

Source Tracking ◽

Neural Network Approach ◽

Heterogeneous Samples ◽

Ontology Structure ◽

Relationship Of ◽

The Relationship ◽

Accuracy Speed

AbstractThe taxonomical structure of microbial community sample is highly habitat-specific, making it possible for source tracking niches where samples are originated. Current methods face challenges when the number of samples and niches are magnitudes more than current in use, under which circumstances they are unable to accurately source track samples in a timely manner, rendering them difficult in knowledge discovery from sub-million heterogeneous samples. Here, we introduce a deep learning method based on Ontology-aware Neural Network approach, ONN4MST (https://github.com/HUST-NingKang-Lab/ONN4MST), which takes into consideration the ontology structure of niches and the relationship of samples from these ontologically-organized niches. ONN4MST’s superiority in accuracy, speed and robustness have been proven, for example with an accuracy of 0.99 and AUC of 0.97 in a microbial source tracking experiment that 125,823 samples and 114 niches were involved. Moreover, ONN4MST has been utilized on several source tracking applications, showing that it could provide highly-interpretable results from samples with previously less-studied niches, detect microbial contaminants, and identify similar samples from ontologically-remote niches, with high fidelity.

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Factors Influencing the Duration of Acute Infantile Diarrhea

Paediatrica Indonesiana ◽

10.14238/pi35.5-6.1995.141-9 ◽

2018 ◽

Vol 35 (5-6) ◽

pp. 141-9

Author(s):

Sutomo Rahardjo ◽

S. M. Salendu Warouw

Keyword(s):

Nutritional Status ◽

Chronic Diarrhea ◽

Health Department ◽

Age Group ◽

Infantile Diarrhea ◽

E Coli ◽

Factors Influencing ◽

Relationship Of ◽

The Relationship ◽

Carbohydrate Intolerance

A retrospective study was conducted on infantile diarrhea treated at the Gunung Wenang General Hospital to evaluate the relationship of age, nutritional status and cause of diarrhea to the duration of episode of infantile diarrhea. From January 1991 up to December 1992, 584 infantile diarrhea cases out of 1109 infants were treated at the Division Gastroenterology Child Health Department. Three hundred and forty-four (58,7%) of them were male, and 56% of patients were less than 12 months of age. The nutritional status was evaluated using NCHS standard; 391 (67,0%) were well-nourished, 49 (8,4%) were moderately under-nourished, and .S (0,8%) were severely malnourished. Duration of diarrhea of 4 days of less was found in 70.8% of patients 13-24 months old, 43.9% in 7-12 months age group, 46.2% of infants 4-6 months age group, and 54.8% of infants 1-3 months age group, 60,6% of well-nourished infants, 56,8% of mildly malnourished infants, and 31,5% of moderate to severely malnourished infants. Chronic diarrhea was found in 5 infants (0,9%), 3 with severe malnourished infants suffered from carbohydrate intolerance with E. histolytica infestation and the other 2 infants due to E. coli.

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Amino acid deprivation and its effect on mating ability inEscherichia coliK12

Genetics Research ◽

10.1017/s0016672300009964 ◽

1966 ◽

Vol 8 (1) ◽

pp. 115-118 ◽

Cited By ~ 1

Author(s):

K. W. Fisher

Keyword(s):

Escherichia Coli ◽

Amino Acids ◽

Amino Acid ◽

Amino Acid Deprivation ◽

Mating Ability ◽

Chromosome Transfer ◽

E Coli ◽

Donor Cells ◽

Relationship Of ◽

The Relationship

The conclusion by Suit, Matney, Doudney & Billen (1964) that Hfr donor cells ofEscherichia coliK12, starved of required amino acids can mate, has been re-examined. It appears that their conclusion is not valid and that apparent fertility of amino-acid starved cells is due to cross-feeding by the F−cells. The relationship of this result to the alternative mechanisms for chromosome transfer inE. coliis discussed.

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