scholarly journals Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor

2020 ◽  
Vol 66 (9) ◽  
pp. 495-504
Author(s):  
Yan Zheng ◽  
Xiaolong Hu ◽  
Zhongjun Jia ◽  
Paul L.E. Bodelier ◽  
Zhiying Guo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Prokaryotic Community ◽  
16S Rrna Gene Analysis ◽  
Pit Mud ◽  
Niche Competition ◽  
Occurrence Patterns ◽  
The 16S Rrna Gene

It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4+, available P, available K, and Ca2+) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Priya Lakra ◽  
Helianthous Verma ◽  
Chandni Talwar ◽  
Durgesh Narain Singh ◽  
Nirjara Singhvi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

scholarly journals Resolving microbial microdiversity with high accuracy full length 16S rRNA Illumina sequencing

2014 ◽  
Author(s):  
Catherine Burke ◽  
Aaron E Darling
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Single Molecule ◽  
Illumina Miseq ◽  
Full Length ◽  
Rrna Gene ◽  
Variable Regions ◽  
Phylogenetic Resolution ◽  
Miseq Platform ◽  
The 16S Rrna Gene

We describe a method for sequencing full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform. The resulting sequences have about 100-fold higher accuracy than standard Illumina reads and are chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. We demonstrate that the data provides fine scale phylogenetic resolution not available from Illumina amplicon methods targeting smaller variable regions of the 16S rRNA gene.

scholarly journals Comparative study on the diversity of endophytic actinobacteria communities from Ficus deltoidea using metagenomic and culturedependent approaches

2018 ◽  
Vol 19 (4) ◽  
pp. 1514-1520 ◽  
Author(s):  
ISRA JANATININGRUM ◽  
DEDY DURYADI SOLIHIN ◽  
ANJA MERYANDINI ◽  
YULIN LESTARI
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Comparative Study ◽  
Herbal Remedies ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Ficus Deltoidea ◽  
Close Relationship ◽  
The 16S Rrna Gene ◽  
Culture Dependent

Janatiningrum I, Solihin DD, Meryandini A, Lestari Y. 2018. Comparative study on the diversity of endophytic actinobacteriacommunities from Ficus deltoidea using metagenomic and culture-dependent approaches. Biodiversitas 19: 1514-1520. Actinobacteriaendophytes of medicinal plants may play an essential role in producing a variety of critical bioactive compounds. However, the possiblecontribution of such actinobacteria to the pharmacological properties of traditional herbal remedies remains mostly unknown. Forexample, the diversity and attributes of actinobacteria endophytes in Ficus deltoidea, a small tree species that has long been used to treatdiseases such as cancer, diabetes, and cardiovascular illnesses, have not been explored. Here, the actinobacteria endophyte communitystructure in F. deltoidea was investigated using both culture-dependent and metagenomics approaches. Based on morphologicalcharacteristics and 16S rRNA gene analysis, the dominant culturable actinobacteria isolates exhibited a close relationship withStreptomyces. The metagenomic technique using PCR-DGGE analysis of the 16S rRNA gene showed the presence of 11 OTUs in F.deltoidea tissue. Whereas the dominant culturable actinobacteria endophytes in F. deltoidea was Streptomyces, the metagenomicapproach showed non-Streptomyces, particularly Rhodococccus and Verrucosispora, to be also important. Thus, results from bothculture-dependent and metagenomic approaches provided useful indicators on the diversity and community structure of actinobacteriaendophytes in F. deltoidea.

scholarly journals Cloning of a Transglutaminase Gene from an Indonesian Streptomyces Strain

2016 ◽  
Vol 11 (1) ◽  
pp. 31
Author(s):  
Seprianto Chaniago
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Library ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Streptomyces Strain ◽  
Microbial Strains ◽  
Encoding Gene ◽  
The 16S Rrna Gene

Microbial Transglutaminase (MTGase, EC 2.3.2.13) is an enzyme that catalyzes the transfer of acyl group. Many microbial strains that produce MTGase belong to Streptomyces members. This research was aimed at cloning of a MTGase gene. PCR–based screening of ten MTGase-producing streptomyces isolates from soil in West Nusa Tenggara led to detection of one potential isolate, designated as TTA 02 SDS 14. The partial  MTGase-encoding gene (470 bp)  was amplified by PCR and sequenced. The sequence result indicate its similarity of 93 % with that of Streptomyces cinnamoneus. The 16S rRNA gene analysis showed its identity as Streptomyces thioleteus. Fosmid-based construction of a genomic library from the isolate  and subsequent screening led to the isolation of  a ~40-Kb fosmid harboring a MTGase gene.

scholarly journals Diversity of the ‘Candidatus Phytoplasma asteris’ and ‘Candidatus Phytoplasma fraxini’ isolates that infect urban trees in Bogotá, Colombia

2020 ◽  
Vol 70 (12) ◽  
pp. 6508-6517 ◽  
Author(s):  
Liliana Franco-Lara ◽  
Jennifer Andrea García ◽  
Yuly Eilen Bernal ◽  
Rubén Adolfo Rodríguez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Pattern ◽  
Urban Trees ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Magnolia Grandiflora ◽  
Urban Tree ◽  
Pcr Rflp ◽  
The 16S Rrna Gene

Phytoplasmas have been associated with a disease that affects trees of at least 11 species from different botanic families in Bogotá, Colombia. ‘Candidatus Phytoplasma asteris’ and ‘Candidatus Phytoplasma fraxini’ are the major groups of phytoplasma in the area of Bogotá. In this study, the genetic diversity within ‘Ca. P. asteris’ and ‘Ca. P. fraxini’ was studied in five urban tree species: Croton species (Euphorbiaceae), Fraxinus uhdei (Oleaceae), Magnolia grandiflora (Magnoliaceae), Populus nigra (Salicaceae) and Quercus humboldtii (Fagaceae). Analyses of the 16S rRNA gene using nested PCR, RFLP and sequencing showed that phytoplasmas of ‘Ca. P. asteris’ could be assigned to: subgroup 16SrI-B; a new subgroup named 16SrI-AF, with a restriction pattern similar to that of 16SrI-B; and a new subgroup named 16SrI-AG, with a restriction pattern similar to that of 16SrI-K and 16SrI-AH with a restriction pattern similar to that of 16SrI-AC. ‘Ca. P. fraxini’ isolates belonged to a new subgroup named 16SrVII-G, with a restriction pattern similar to that of 16SrVII-A. To complement the identification of the phytoplasma strains, we amplified nonribosomal genes such as leuS and secA. Unexpectedly, it was observed that in 16 trees in which 16S rRNA gene analysis showed the presence of ‘Ca. P. fraxini’ only, the leuS or secA primers amplified sequences exclusively affiliated to ‘Ca. P. asteris. In those plants, sequences belonging to ‘Ca. P. fraxini’ leuS or secA genes were not amplified. The present work contributes to the identification of novel strains of both species in Colombia, and supports previous suggestions that phytoplasmas in South America are highly variable.

scholarly journals Molecular identification of a new isolate of actinobacteria ATIS61 and characterization of the protease activities

2021 ◽  
Vol 22 (3) ◽  
Author(s):  
FADHLIAH AMFAR ◽  
Lenni Fitri ◽  
SUHARTONO SUHARTONO
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Identification ◽  
Protease Activity ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Peptide Bonds ◽  
Activity Test ◽  
The 16S Rrna Gene

Abstract. Amfar F, Fitri L, Suhartono. 2021. Molecular identification of a new isolate of actinobacteria ATIS61 and characterization of the protease activities. Biodiversitas 22: 1564-1569. Protease is an enzyme that catalyzes the hydrolysis of peptide bonds in protein. Actinobacteria are one of bacterial groups that is able to produce protease. Actinobacteria are Gram-positive bacteria and mostly aerobic. This study aimed to identify protease-producing actinobacteria ATIS61 isolate using 16S rRNA gene and to characterize the protease activity. This study was experimental research, consisted of amplification and sequencing of the 16S rRNA gene, and protease activity test. The 16S rRNA gene analysis showed that ATIS61 isolate was closely related to Nocardia sp. strain 335427 with a 99.88% similarity and the result of phylogenetic tree construction was related to Nocardia farcinica strain ARS8 with Bootstrap 94%. Protease activity test showed the highest activity was on the eighth day of incubation at 0.115 U/mL. Protease activity based on temperature showed the highest activity at 40°C of 0.156 U/mL and the stability of protease towards temperature was stable at 40°C and 50°C. Protease activity showed that the highest protease activity was at pH 8 of 0.096 U/mL and the highest protease stability was also at pH 8. The addition of HgCl2 showed that it could inhibit protease activity with a value of 0.059 U/mL.

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

Sign in / Sign up

Export Citation Format

Share Document