Moderate thermophilic chemoorganoheterotrophic bacterium in surface layer of anthropogenic grounds of industrial estate area of Al-Mafraq, Jordan

Surface of oil-contaminated soil from Industrial Estate of Al-Mafraq city, Jordan, was investigated for the presence of aerobic oil-degrading moderately thermophilic bacteria. A pure culture of spore forming aerobic chemoorganogeterotrophic rod shaped bacterial isolate, designated as strain j3n, was obtained. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain j3n is closely related to gram-positive bacteria of kaustophilus thermoleovorans cluster of Geobacillus genus. Strain j3n grew aerobically with oil, hexadecane, benzoate and acetate. Growth data indicated that utilization of hexadecane but not of oil and benzoate might be under catabolite repression control. Possibility of a regulation of alkane degradation by acetate in aerobic thermophilic gram-positive bacteria of Geobacillus spp. was shown for the first time.

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Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Animal Microbiome ◽

10.1186/s42523-021-00074-8 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sesilje Weiss ◽

David Taggart ◽

Ian Smith ◽

Kristofer M. Helgen ◽

Raphael Eisenhofer

Keyword(s):

Microbial Community ◽

Reproductive Cycle ◽

Tammar Wallaby ◽

The Body ◽

Rrna Gene ◽

Microbial Composition ◽

Birth Canal ◽

Gram Positive Bacteria ◽

Rigorous Framework ◽

The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

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Identification of Poly(cis-1,4-Isoprene) Degradation Intermediates during Growth of Moderately Thermophilic Actinomycetes on Rubber and Cloning of a Functional lcp Homologue from Nocardia farcinica Strain E1

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3375-3382.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3375-3382 ◽

Cited By ~ 58

Author(s):

Ebaid M. A. Ibrahim ◽

Matthias Arenskï¿½tter ◽

Heinrich Luftmann ◽

Alexander Steinbï¿½chel

Keyword(s):

Thermophilic Bacteria ◽

Natural Rubber Latex ◽

Gel Permeation Chromatography ◽

Mycolic Acid ◽

Rrna Gene ◽

Ionization Mass ◽

Thermophilic Actinomycetes ◽

Moderately Thermophilic ◽

Nocardia Farcinica ◽

Different Strains

ABSTRACT The enrichment and isolation of thermophilic bacteria capable of rubber [poly(cis-1,4-isoprene)] degradation revealed eight different strains exhibiting both currently known strategies used by rubber-degrading mesophilic bacteria. Taxonomic characterization of these isolates by 16S rRNA gene sequence analysis demonstrated closest relationships to Actinomadura nitritigenes, Nocardia farcinica, and Thermomonospora curvata. While strains related to N. farcinica exhibited adhesive growth as described for mycolic acid-containing actinomycetes belonging to the genus Gordonia, strains related to A. nitritigenes and T. curvata formed translucent halos on natural rubber latex agar as described for several mycelium-forming actinomycetes. For all strains, optimum growth rates were observed at 50ï¿½C. The capability of rubber degradation was confirmed by mineralization experiments and by gel permeation chromatography (GPC). Intermediates resulting from early degradation steps were purified by preparative GPC, and their analysis by infrared spectroscopy revealed the occurrence of carbonyl carbon atoms. Staining with Schiff's reagent also revealed the presence of aldehyde groups in the intermediates. Bifunctional isoprenoid species terminated with a keto and aldehyde function were found by matrix-assisted laser desorption ionization-time-of-flight and electrospray ionization mass spectrometry analyses. Evidence was obtained that biodegradation of poly(cis-1,4-isoprene) is initiated by endocleavage, rather than by exocleavage. A gene (lcp) coding for a protein with high homology to Lcp (latex-clearing protein) from Streptomyces sp. strain K30 was identified in Nocardia farcinica E1. Streptomyces lividans TK23 expressing this Lcp homologue was able to cleave synthetic poly(cis-1,4-isoprene), confirming its involvement in initial polymer cleavage.

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Fusobacterium nucleatum, the first Gram-negative bacterium demonstrated to produce polyglutamate

Canadian Journal of Microbiology ◽

10.1139/w09-003 ◽

2009 ◽

Vol 55 (5) ◽

pp. 627-632 ◽

Cited By ~ 33

Author(s):

Thomas Candela ◽

Marie Moya ◽

Michel Haustant ◽

Agnès Fouet

Keyword(s):

In Silico Analysis ◽

Fusobacterium Nucleatum ◽

Gram Negative Bacteria ◽

Negative Bacterium ◽

Gram Positive ◽

Gram Negative ◽

Gram Positive Bacteria ◽

The Third ◽

Gram Negative Organisms ◽

First Time

Poly-γ-glutamate has been described in many Gram-positive organisms. When anchored to the surface, it is a capsule and as such a virulence factor. Based on sequence similarities, few Gram-negative organisms have been suggested to synthesize poly-γ-glutamate. For the first time, a Gram-negative bacterium, Fusobacterium nucleatum , is shown to produce and secrete poly-γ-glutamate. Putative poly-γ-glutamate-synthesizing genes from Gram-negative organisms have been compared with their Gram-positive homologs by in silico analysis, i.e., gene sequence and phylogenetic analysis. Clusters of three instead of four genes were highlighted by our screen. The products of the first two genes display similarity with their Gram-positive equivalents, yet the sequences from the Gram-negative organisms can be distinguished from those of the Gram-positives. Interestingly, the sequence of the predicted product of the third gene is conserved among Gram-negative bacteria but displays no similarity to that of either the third or fourth gene of the Gram-positive operons. It is suggested that, like for Gram-positive bacteria, poly-γ-glutamate has a role in virulence for pathogens and one in survival for other Gram-negative bacteria.

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Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments

Applied and Environmental Microbiology ◽

10.1128/aem.02811-06 ◽

2007 ◽

Vol 73 (10) ◽

pp. 3272-3282 ◽

Cited By ~ 220

Author(s):

Erin A. Gontang ◽

William Fenical ◽

Paul R. Jensen

Keyword(s):

New Taxa ◽

Marine Sediments ◽

Sequence Data ◽

Rrna Gene ◽

Gram Positive ◽

Gram Positive Bacteria ◽

Operational Taxonomic Units ◽

The Republic ◽

Republic Of Palau ◽

High Degree

ABSTRACT Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class Actinobacteria while the remaining 65 (34.4%) were members of the class Bacilli. Using a sequence identity value of ≥98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.

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The antimicrobial potentialities of (Nk-lysin peptides of chicken, bovine, and human) against bacteria and rotavirus

10.21203/rs.3.rs-409635/v1 ◽

2021 ◽

Author(s):

Maged. M Mahmoud ◽

Ahmed M. Al-Hejin ◽

Turki S Abujaml ◽

S Abd-Elmaksoud ◽

Salem M. El-Hamidy ◽

...

Keyword(s):

Antiviral Activity ◽

Klebsiella Oxytoca ◽

Bacterial Strains ◽

Gram Positive ◽

Gram Negative ◽

Beta Lactamases ◽

Gram Positive Bacteria ◽

The Past ◽

Antiviral Activities ◽

First Time

Abstract For the first time, this study was carried out to investigate and evaluate the relative antibacterial activity of three different Nk-lysin peptides from human, chicken, and bovine activity compared to Gram-negative and Gram-positive bacteria as well as antiviral activity against rotavirus (strain SA-11) and finally mechanisms of action optionality. This report is the first of its kind that investigates the increased antimicrobial ability of (Nk-lysin + AgNPs) and (Nk-lysin + human IL-2) combinations against S. typhi activity by carrying out direct comparison under similar experimental settings. Our results showed that gram-negative and gram-positive microorganisms, including Streptococcus pyogenes, Streptococcus mutans, Escherichia coli, Pseudomonas aeruginosa, Klebsiella oxytoca, Shigella sonnei, Klebsiella pneumoniae and Salmonella typhimurium, are susceptible to NK-lysin treatment. It was shown in our findings that there was equal potentiality in mixture (Nk-lysin + AgNPs) and (Nk-lysin + human IL-2) for preventing the growth of S. typhi, however, when added together, there was minor increase in the level of action. In our study, the TOHO-1 gene was absent in treated bacteria. Following treatment with Nk-lysin peptides, the beta-lactamases genes (CTX-M-1, M-8, and M-9) were not found in any bacterial strains. The examination did not find any of the plasmid mediated quinolone resistance genes in the bacterial strains as a response to NK-lysin treatment. Nonetheless, no study has been carried out in the past that characterized the antiviral activity of bovine, human and chicken Nk-lysin peptides. Hence, this is the foremost study on the enhanced antimicrobial activity of human, bovine and chicken Nk-lysin peptides against Rotavirus (strain SA-11). The findings of the study demonstrated that the powerful antiviral activities were exhibited by Nk-lysin peptides against Rotavirus (strain SA-11). Based on the comparison between these peptides, it can be concluded that there is an evident potent antiviral activity of bovine Nk-lysin against Rotavirus (strain SA-11) as it restrains infection by up to 90%. However, growth was restricted by 80% by chicken Nk-lysin and by 50% by the human peptide.

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Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa043 ◽

2020 ◽

Vol 96 (4) ◽

Cited By ~ 2

Author(s):

César Ruiz ◽

Marcela Villegas-Plazas ◽

Olivier P Thomas ◽

Howard Junca ◽

Thierry Pérez

Keyword(s):

Extreme Environments ◽

Amplicon Sequencing ◽

Sponge Species ◽

Rrna Gene ◽

Microbiome Composition ◽

16S Amplicon Sequencing ◽

Ecological Success ◽

Specific Community ◽

First Time ◽

The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

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Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65013-0 ◽

2007 ◽

Vol 57 (9) ◽

pp. 2037-2051 ◽

Cited By ~ 143

Author(s):

M. Martini ◽

I.-M. Lee ◽

K. D. Bottner ◽

Y. Zhao ◽

S. Botti ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Tree ◽

Ribosomal Protein ◽

Phylogenetic Analyses ◽

Rflp Analysis ◽

Rrna Gene ◽

Gene Sequences ◽

Gram Positive ◽

The 16S Rrna Gene

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.

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Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.070151-0 ◽

2015 ◽

Vol 65 (Pt_2) ◽

pp. 549-555 ◽

Cited By ~ 54

Author(s):

O. L. Kovaleva ◽

A. Yu. Merkel ◽

A. A. Novikov ◽

R. V. Baslerov ◽

S. V. Toshchakov ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Hot Springs ◽

Thermophilic Bacteria ◽

Physiological Data ◽

Rrna Gene ◽

Content Type ◽

Moderately Thermophilic ◽

Link Type

Three strains of facultatively aerobic, moderately thermophilic bacteria were isolated from terrestrial hot springs in Baikal Lake region and Kamchatka (Russia). Cells of the new isolates were cocci reproducing by binary fission. The temperature range for growth was between 20 and 56 °C and the pH range for growth from pH 4.5 to 8.5, with optimal growth at 47–50 °C and pH 7.0–7.5. The organisms were chemoheterotrophs preferring sugars and polysaccharides as growth substrates. 16S rRNA gene sequences of strains 2842, 2813 and 2918Kr were nearly identical (99.7–100 % similarity) and indicated that the strains belonged to the phylum Planctomycetes . The phylogenetically closest cultivated relatives were Algisphaera agarilytica 06SJR6-2T and Phycisphaera mikurensis FYK2301M01T with 16S rRNA gene sequence similarity values of 82.4 and 80.3 %, respectively. The novel strains differed from them by higher growth temperature, sensitivity to NaCl concentration above 3.0 % and by their cellular fatty acids profile. On the basis of phylogenetic and physiological data, strains 2842T, 2813 and 2918Kr represent a novel genus and species for which we propose the name Tepidisphaera mucosa sp. nov. The type strain is 2842T ( = VKM B-2832T = JCM 19875T). We also propose that Tepidisphaera gen. nov. is the type genus of a novel family, Tepidisphaeraceae fam. nov. and a novel order, Tepidisphaerales ord. nov.

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Molecular and serological detection of Ehrlichia canis in naturally exposed dogs in Iran: an analysis on associated risk factors

Revista Brasileira de Parasitologia Veterinária ◽

10.1590/s1984-29612014002 ◽

2014 ◽

Vol 23 (1) ◽

pp. 16-22 ◽

Cited By ~ 10

Author(s):

Nadi Maazi ◽

Abdolali Malmasi ◽

Parviz Shayan ◽

Seyed Mahdi Nassiri ◽

Taghi Zahraei Salehi ◽

...

Keyword(s):

Risk Factors ◽

Rural Areas ◽

Ehrlichia Canis ◽

Rrna Gene ◽

Igg Antibodies ◽

Serological Detection ◽

Blood Samples ◽

Associated Risk Factors ◽

First Time ◽

The 16S Rrna Gene

The general aim of this study, which was conducted for the first time in Iran, was to evaluate the seroprevalence and geographical distribution of Ehrlichia canis in a dog population in Iran, followed by molecular confirmation using PCR and sequencing. Blood samples were collected from 240 dogs in different areas of Alborz and Tehran Provinces and initially analyzed using the immunofluorescent antibody (IFA) test to detect anti-Ehrlichia canis IgG antibodies. Subsequently, nested PCR was performed based on a fragment of the 16S rRNA gene of E. canis on serologically positive samples. The results showed that 40/240 dogs (16.6%) presented anti-Ehrlichia canis IgG antibodies and that nine of the blood samples from the 40 seropositive dogs (22.5%) contained E. canis DNA, which was confirmed by sequencing. The seroprevalence of E. canis tended to be higher in purebred, one to three-year-old male dogs living in the Plain zone, in rural areas; however, this difference was not statistically significant.

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Isolation and Identification ofAcholeplasmasp. from the Mud Crab,Scylla serrata

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2011/209406 ◽

2011 ◽

Vol 2011 ◽

pp. 1-5 ◽

Cited By ~ 3

Author(s):

Ji-Gang Chen ◽

Dan Lou ◽

Ji-Fang Yang

Keyword(s):

Cell Wall ◽

Scylla Serrata ◽

Rrna Gene ◽

Mud Crab ◽

Isolation And Identification ◽

A Cell ◽

First Time ◽

The 16S Rrna Gene ◽

Ferment Glucose ◽

Mud Crabs

For the first time, a mollicute-like organism (MLO) was cultured from moribund mud crabs (Scylla serrata) during an outbreak of clearwater disease in Zhejiang Province, China. The MLO displayed a fried-egg colony morphology in culture, did not possess a cell wall, and was not retained by 0.45 μm and 0.2 μm filters. It was able to ferment glucose, sucrose, lactose, and maltose, but it did not utilize arginine and urea. The MLO grew in the absence of bovine serum and was not susceptible to digitonin. Sequence analysis of the 16S rRNA gene revealed that this MLO had 99% identity withAcholeplasma laidlawiiPG-8A, which indicates that the organism isolated from mud crabs is a member of the genusAcholeplasma.

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