Microbial community of salt crystals processed from Mediterranean seawater based on 16S rRNA analysis

2010 ◽  
Vol 56 (1) ◽  
pp. 44-51 ◽  
Author(s):  
Houda Baati ◽  
Sonda Guermazi ◽  
Neji Gharsallah ◽  
Abdelghani Sghir ◽  
Emna Ammar
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Sequence Similarity ◽  
Archaeal Community ◽  
Solar Saltern ◽  
16S Rrna Sequence ◽  
16S Rrna Analysis ◽  
Operational Taxonomic Units ◽  
Local Diversity ◽  
Salt Crystals

Phylogenetic analysis of 16S rRNA was used to investigate for the first time the structure of the microbial community that inhabits salt crystals retrieved from the bottom of a solar saltern, located in the coastal area of the Mediterranean Sea (Sfax, Tunisia). This community lives in an extremely salty environment of 250–310 g/L total dissolved salt. A total of 78 bacterial 16S rRNA clone sequences making up to 21 operational taxonomic units (OTUs), determined by the DOTUR program to 97% sequence similarity, was analyzed. These OTUs were affiliated to Bacteroidetes (71.4% of OTUs), and γ-Proteobacteria and α-Proteobacteria (equally represented by 14.2% of the OTUs observed). The archaeal community composition appeared more diverse with 68 clones, resulting in 44 OTUs, all affiliated with the Euryarchaeota phylum. Of the bacterial and archaeal clones showing <97% 16S rRNA sequence identity with sequences in public databases, 47.6% and 84.1% respectively were novel clones. Both rarefaction curves and diversity measurements (Simpson, Shannon–Weaver, Chao) showed a more diverse archaeal than bacterial community at the Tunisian solar saltern pond. The analysis of an increasing clone’s number may reveal additional local diversity.

Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern

2011 ◽  
Vol 57 (12) ◽  
pp. 975-981 ◽  
Author(s):  
Houda Baati ◽  
Raja Jarboui ◽  
Néji Gharsallah ◽  
Abdelghani Sghir ◽  
Emna Ammar
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Archaeal Community ◽  
Community Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Solar Saltern ◽  
16S Rrna Gene Analysis ◽  
Operational Taxonomic Units

The microbial community of a magnesium-rich bittern brine saturated with NaCl (380–400 g/L) from a Tunisian solar saltern was investigated using a molecular approach based on 16S rRNA gene analysis and viability tests. The results revealed the existence of microbial flora. Viability test assessment showed that 46.4% of this flora was viable but not detectable by culturability tests. 16S rRNA genes from 49 bacterial clones and 38 archaeal clones were sequenced and phylogenetically analyzed. Eleven operational taxonomic units (OTUs) determined by the DOTUR program with 97% sequence similarity were generated for Bacteria. These OTUs were affiliated with Bacteroidetes and Gammaproteobacteria. The archaeal community composition exhibited more diversity with 38 clones, resulting in 13 OTUs affiliated with the Euryarchaeota phylum. Diversity measurement showed a more diverse archaeal than bacterial community at the saturated pond.

Aggregatimonas Sangjinii Gen. Nov., Sp. Nov., A Novel Silver Nanoparticle Synthesizing Bacterium Belonging to the Family Flavobacteriaceaee

2021 ◽  
Author(s):  
Dawoon Chung ◽  
Jaoon Young Hwan Kim ◽  
Kyung Woo Kim ◽  
Yong Min Kwon
Keyword(s):  
16S Rrna ◽  
Genome Sequence ◽  
Sequence Similarity ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
The Family ◽  
The Media

Abstract A gram-negative, orange-pigmented, non-flagellated, gliding, rod-shaped, and aerobic bacterium, designated strain F202Z8T, was isolated from a rusty iron plate found in the intertidal region of Taean, South Korea. Notably, this strain synthesized silver nanoparticles (AgNPs), and 17 putative genes responsible for the synthesis of AgNPs were found in its genome. The complete genome sequence of strain F202Z8T is 4,723,614 bp, with 43.26% G + C content. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain F202Z8T forms a distinct lineage with closely related genera Maribacter, Pelagihabitans, Pseudozobellia, Zobellia, Pricia, and Costertonia belonging to the family Flavobacteriaceae. The 16S rRNA sequence similarity was < 94.5%. The digital DNA–DNA hybridization and average nucleotide identity values calculated from the whole genome-sequence comparison between strain F202Z8T and other members of the family Flavobacteriaceae were in the ranges of 12.7–16.9% and 70.3–74.4%, respectively. Growth was observed at 15–33°C (optimally at 30°C), at pH 6.5–7.5 (optimally at pH 7.0), and with the addition of 2.5–4.5% (w/v) NaCl to the media (optimally at 4.0%). The predominant cellular fatty acids were iso-C15: 0, iso-C15 :1 G, and iso-C17 :0 3-OH; the major respiratory quinone was MK-6. Polar lipids included phosphatidylethanolamine, five unidentified lipids, and two unidentified aminolipids. Our polyphasic taxonomic results suggested that this strain represents a novel species of a novel genus in the family Flavobacteriaceae, for which the name Aggregatimonas sangjinii gen. nov., sp. nov. is proposed. The type strain of Aggregatimonas sangjinii is F202Z8T (= KCCM 43411T = LMG 31494T).

Facklamia lactis sp. nov., isolated from raw milk

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Etienne V. Doll ◽  
Lena Staib ◽  
Christopher Huptas ◽  
Siegfried Scherer ◽  
Mareike Wenning
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Raw Milk ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Genome Phylogeny

Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466T (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842T (96.9 %), and Facklamia hominis CCUG 36813T (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301T and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301T and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301T are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10–40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l−1 yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301T (=DSM 111018T=LMG 31861T) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.

scholarly journals Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hussein Anani ◽  
Rita Abou Abdallah ◽  
May Khoder ◽  
Anthony Fontanini ◽  
Morgane Mailhe ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Left Colon ◽  
Deficiency Anemia ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Sequence ◽  
A Genome ◽  
The Family ◽  
Bacterium Strain

AbstractThe gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.

scholarly journals Marinobacter salicampi sp. nov., isolated from a marine solar saltern in Korea

2007 ◽  
Vol 57 (9) ◽  
pp. 2102-2105 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
The Novel ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, motile, rod-shaped, Marinobacter-like bacterial strain, ISL-40T, was isolated from a marine solar saltern of the Yellow Sea in Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. Strain ISL-40T grew optimally at pH 7.0–8.0 and at 30 °C. It contained Q-9 as the predominant ubiquinone. The major fatty acids were C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and 10-methyl C16 : 0. The DNA G+C content was 58.1 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-40T belongs to the genus Marinobacter. Strain ISL-40T exhibited 16S rRNA gene sequence similarity values of 93.5–96.4 % to the type strains of recognized Marinobacter species. The differential phenotypic properties and phylogenetic distinctiveness of strain ISL-40T revealed that it is separate from recognized Marinobacter species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain ISL-40T represents a novel species of the genus Marinobacter, for which the name Marinobacter salicampi sp. nov. is proposed. The type strain is ISL-40T (=KCTC 12972T=CCUG 54357T).

scholarly journals Alkalibacillus flavidus sp. nov., isolated from a marine solar saltern

2010 ◽  
Vol 60 (2) ◽  
pp. 434-438 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Phenotypic Properties ◽  
Diamino Acid

A Gram-stain-positive, motile, rod-shaped bacterial strain, ISL-17T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain ISL-17T grew optimally at pH 8.5–9.0, at 37 °C and in the presence of approximately 10 % (w/v) NaCl. It contained meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, MK-7 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The DNA G+C content was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-17T fell within the genus Alkalibacillus, clustering with Alkalibacillus salilacus BH163T with a bootstrap resampling value of 100 %. Strain ISL-17T exhibited 98.2 % 16S rRNA gene sequence similarity to A. salilacus BH163T and 95.8–96.5 % similarity to the type strains of the other Alkalibacillus species. The mean DNA–DNA relatedness value between strain ISL-17T and A. salilacus KCTC 3916T was 19 %. The phenotypic properties of strain ISL-17T, together with its phylogenetic and genetic distinctiveness, enable this strain to be differentiated from recognized Alkalibacillus species. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-17T represents a novel species within the genus Alkalibacillus, for which the name Alkalibacillus flavidus sp. nov. is proposed; the type strain is ISL-17T (=KCTC 13258T =CCUG 56753T).

scholarly journals Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora

1999 ◽  
Vol 65 (8) ◽  
pp. 3287-3292 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Chih-Ching Chien ◽  
Bruce J. Paster ◽  
Rebecca L. Ericson ◽  
Roger P. Orcutt ◽  
...  
Keyword(s):  
16S Rrna ◽  
Single Species ◽  
Rapid Identification ◽  
Sequence Information ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
16S Rrna Analysis ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The “altered Schaedler flora” (ASF) was developed for colonizing germfree rodents with a standardized microbiota. The purpose of this study was to identify each of the eight ASF strains by 16S rRNA sequence analysis. Three strains were previously identified asLactobacillus acidophilus (strain ASF 360),Lactobacillus salivarius (strain ASF 361), andBacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rRNA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequences of the type strains of Lactobacillus murinis and Lactobacillus animalis (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus andLactobacillus lactis. Strain ASF 519 falls into an unnamed genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacteroides] forsythus, and CDC group DF-3. This unnamed genus is in theCytophaga-Flavobacterium-Bacteroides phylum and is most closely related to the genus Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexistipesphylum and exhibits sequence identity with rodent isolates of Robertson. The remaining four ASF strains, which are extremely oxygen-sensitive fusiform bacteria, group phylogenetically with the low-G+C-content gram-positive bacteria (Firmicutes,Bacillus-Clostridium group). ASF 356, ASF 492, and ASF 502 fall into Clostridium cluster XIV of Collins et al. Morphologically, ASF 492 resembles members of this cluster,Roseburia cecicola, and Eubacterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to that of E. plexicaudatum. Since the type strain and other viable original isolates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gram-positive phylogenetic tree but is not closely related to any organisms whose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid identification of ASF strains and should permit detailed analysis of the interactions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms.

Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1089-1095 ◽  
Author(s):  
Markus Haber ◽  
Sigal Shefer ◽  
Assunta Giordano ◽  
Pierangelo Orlando ◽  
Agata Gambacorta ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Sea Salts ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The Mediterranean

Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family Flavobacteriaceae within the phylum Bacteroidetes , with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family Flavobacteriaceae , for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.

scholarly journals Alcanivorax pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium

2011 ◽  
Vol 61 (6) ◽  
pp. 1370-1374 ◽  
Author(s):  
Qiliang Lai ◽  
Liping Wang ◽  
Yuhui Liu ◽  
Yuanyuan Fu ◽  
Huanzi Zhong ◽  
...  
Keyword(s):  
16S Rrna ◽  
Deep Sea ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Close Relation ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
16S Rrna Sequence ◽  
Deep Sea Sediment ◽  
The Pacific

A taxonomic study was carried out on a novel bacterial strain, designated W11-5T, which was isolated from a pyrene-degrading consortium enriched from deep-sea sediment of the Pacific Ocean. The isolate was Gram-reaction-negative and oxidase- and catalase-positive. Growth was observed in 0.5–12 % (w/v) NaCl and at 10–42 °C. On the basis of 16S rRNA gene sequence analysis, strain W11-5T was shown to belong to the genus Alcanivorax with a close relation to A. dieselolei B-5T (93.9 % 16S rRNA sequence similarity), A. balearicus MACL04T (93.1 %), A. hongdengensis A-11-3T (93.1 %), A. borkumensis SK2T (93.0 %), A. venustensis ISO4T (93.0 %) and A. jadensis T9T (92.9 %). Similarities between the gyrB gene sequences of W11-5T and other species of the genus Alcanivorax were between 76.8 and 80.8 %. The principal fatty acids were C12 : 0 3-OH (8.0 %), C16 : 0 (29.1 %) and C18 : 1ω7c (27.4 %). The G+C content of the chromosomal DNA was 60.8 mol%. Based on its morphology, physiology and fatty acid composition as well as the results of 16S rRNA and gyrB gene sequence analyses, strain W11-5T ( = MCCC 1A00474T  = CCTCC AB 208236T  = LMG 25514T) represents a novel species of the genus Alcanivorax, for which the name Alcanivorax pacificus sp. nov. is proposed.

scholarly journals Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade

2007 ◽  
Vol 57 (2) ◽  
pp. 270-275 ◽  
Author(s):  
Dong H. Choi ◽  
Jang-Cheon Cho ◽  
Brian D. Lanoil ◽  
Stephen J. Giovannoni ◽  
Byung C. Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sargasso Sea ◽  
The Novel ◽  
Solar Saltern ◽  
The Family

Two strictly aerobic, Gram-negative bacteria, designated strains CL-SP27T and B5-6T, were isolated from the hypersaline water of a solar saltern in Korea and from the surface water of the Sargasso Sea, respectively. The two strains were rod-shaped, non-motile and grew on marine agar 2216 as beige colonies. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation of the novel strains to the family Rhodobacteraceae. However, the novel strains were only distantly related to members of the Roseobacter clade, forming a distinct lineage. Although the 16S rRNA gene sequence similarity between strains CL-SP27T and B5-6T was very high (99.6 %), DNA–DNA relatedness between the strains was 48.4 %, suggesting that the strains be categorized as two genospecies. Additionally, the two novel strains could be differentiated by DNA G+C contents, fatty acid profiles, carbon source utilization patterns, antibiotic susceptibilities and biochemical characteristics. Based on taxonomic data obtained in this study, strains CL-SP27T and B5-6T represent separate species within a novel genus of the family Rhodobacteraceae, for which the names Maribius salinus gen. nov., sp. nov. (type species) and Maribius pelagius sp. nov. are proposed. The type strains of Maribius salinus and Maribius pelagius are CL-SP27T (=KCCM 42113T=JCM 13037T) and B5-6T (=KCCM 42336T=JCM 14009T), respectively.

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