scholarly journals Taxonomy Analysis in Bacteria Kingdom based on Protein Domain: A Comparison Study

2021 ◽  
Author(s):  
Boqian Wang ◽  
Jianglin Zhou ◽  
Yuan Jin ◽  
Mingda Hu ◽  
Yunxiang Zhao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Tree ◽  
Direct Relationship ◽  
Biological Significance ◽  
Protein Domain ◽  
Functional Domain ◽  
Ncbi Taxonomy ◽  
Comparison Study ◽  
Conserved Genes ◽  
Complete Framework

It is important to conduct taxonomy research on the bacteria kingdom for deeper understanding, which can utilize the conserved genes, 16s rRNA, protein domain, and so on. Among them, the methods based on the protein domain has a direct relationship with phenotype. However, these methods still lack analysis of their biological significance, models evaluation and the comparison of taxonomy results. To this end, we propose a complete framework to standardize the process for taxonomy problem based on the protein functional domain. By applying it to bacteria kingdom and comparing the results with the NCBI taxonomy, we point out the most appropriate method in each step of the framework and evaluate models according to the biological significance. Finally, taxonomy suggestions and recommendations are proposed based on the phylogenetic tree generated by the framework with the most appropriate combination.

scholarly journals Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content

2018 ◽  
Author(s):  
Jasper J. Koehorst ◽  
Edoardo Saccenti ◽  
Vitor Martins dos Santos ◽  
Maria Suarez-Diez ◽  
Peter J. Schaap
Keyword(s):  
16S Rrna ◽  
Functional Diversity ◽  
Large Scale ◽  
Protein Domain ◽  
Functional Domain ◽  
16S Rrna Sequence ◽  
Gene 16S Rrna ◽  
Sigmoid Curve ◽  
Bacterial Genes ◽  
New Applications

ABSTRACTBackgroundThe omnipresent 16S ribosomal RNA gene (16S-rRNA) is commonly used to identify and classify bacteria though it does not take into account the distinctive functional characteristics of taxa. We explored functional domain landscapes of over 5700 complete bacterial genomes, representing a wide coverage of the bacterial tree of life, and investigated to what extent the observed protein domain diversity correlates with the expected evolutionary diversity, using 16S-rRNA as metric for evolutionary distance.ResultsAnalysis of protein domains showed that 83% of the bacterial genes code for at least one of the 9722 domain classes identified. By comparing clade specific and global persistence scores, candidate horizontal gene transfer and signifying domains could be identified. 16S-rRNA and functional domain content distances were used to evaluate and compare species divergence and overall a sigmoid curve is observed. Already at close 16S-rRNA evolutionary distances, high levels of functional diversity can be observed. At a larger 16S-rRNA distance, functional differences accumulate at a relatively lower pace.ConclusionsAnalysis of 16S-rRNA sequences in the same taxa suggests that, in many cases, additional means of classification are required to obtain reliable phylogenetic relationships. Whole genome protein domain class phylogenies correlate with, and complement 16S-rRNA sequence-based phylogenies. Moreover, domain-based phylogenies can be constructed over large evolutionary distances and provide an in-depth insight of the functional diversity within and among species and enables large scale functional comparisons. The increased granularity obtained paves way for new applications to better predict the relationships between genotype, physiology and ecology.

The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny

1989 ◽  
Vol 35 (1) ◽  
pp. 141-147 ◽  
Author(s):  
R. Amils ◽  
L. Ramírez ◽  
J. L. Sanz ◽  
I. Marín ◽  
A. G. Pisabarro ◽  
...  
Keyword(s):  
Functional Analysis ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Functional Information ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Sequence Comparisons ◽  
Free System ◽  
Translation Apparatus ◽  
Evolutionary Clock

Forty different antibiotics with diverse kingdom and functional specificities were used to measure the functional characteristics of the archaebacterial translation apparatus. The resulting inhibitory curves, which are characteristic of the cell-free system analyzed, were transformed into quantitative values that were used to cluster the different archaebacteria analyzed. This cluster resembles the phylogenetic tree generated by 16S rRNA sequence comparisons. These results strongly suggest that functional analysis of an appropriate evolutionary clock, such as the ribosome, is of intrinsic phylogenetic value. More importantly, they indicate that the study of the nexus between genotypic and phenotypic (functional) information may shed considerable light on the evolution of the protein synthetic machinery.Key words: antibiotics, ribosomes, archaebacteria, phylogeny, functional analysis.

scholarly journals Molecular identification and genotyping of Atopobium vaginae, 16s rRNA gene from Bacterial Vaginosis miscarriage women in AL-Hillah city

2013 ◽  
Vol 11 (01) ◽  
pp. 74-82
Author(s):  
Ilham A. Bunyan ◽  
Asmaa K. Gatea ◽  
Alaa K. Hameed
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Rrna Gene ◽  
City Hospital ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Columbia Blood Agar ◽  
The 16S Rrna Gene ◽  
Atopobium Vaginae

This study was aimed to determine the Atopobium vaginae associated BV in vaginosis women and women with miscarriage. Also other aim, the DNA sequencing was performed for phylogenetic tree analysis of 16SrRNA gene in local Atopobium vaginae isolates in comparison with NCBI-Genbank global Atopobium vaginae isolates and finally submission of the present isolates in NCBI-Genbank database. One hundred fifty (150) high vaginal swabs were collected from women with vaginosis(Seventy five samples were taken from married vaginosis women without miscarriage and Seventy five samples from vaginosis women with miscarriage) from Babylon city hospital and private clinics. The age of patient (15– 45) years. The sample was collected by disposable swabs, genomic DNA was extracted from these swabs. 16s rRNA gene detection by polymerase chain reaction technique . Atopobium vaginae was isolated on Columbia blood agar supplemented with antibiotic for the first time in Iraq, the study confirmed that 9 (12.00%) and 5(6.66%) of Atopobium vaginae out of 150 swabs isolated from miscarriage and non-miscarriage vaginosis women respectively. According to the detection of the 16S rRNA gene, the study revealed that 69(92.00%)and 47(62.66%)of Atopobium vaginae out of 150 swabs obtained from miscarriage and non-miscarriage vaginosis women respectively. BLAST analysis showed that the 16S rRNA gene shared more than 98- 99% sequence compatibility with the sequences of Atopobium vaginae. Furthermore, the phylogenetic tree analysis of the 16S rRNA gene indicated that local Atopobium vaginae (NO.1 and NO. 2 ) isolates shared higher homology with other Atopobium vaginae isolates available in the GenBank. The homology of the nucleotides was between (99.17% and 98.75%) respectively.

scholarly journals Phylogenetic tree analysis for Bali Cattle based on partial sequence 16S rRNA Mitochondrial DNA

2022 ◽  
Vol 335 ◽  
pp. 00014
Author(s):  
R. Misrianti ◽  
S.H. Wijaya ◽  
C. Sumantri ◽  
J. Jakaria
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Partial Sequence ◽  
Bos Grunniens ◽  
Bos Javanicus ◽  
Mitochondria Dna ◽  
Bali Cattle

Mitochondria DNA (mtDNA) as a source of genetic information based on the maternal genome, can provide important information for phylogenetic analysis and evolutionary biology. The objective of this study was to analyze the phylogenetic tree of Bali cattle with seven gene bank references (Bos indicus, Bos taurus, Bos frontalis, and Bos grunniens) based on partial sequence 16S rRNA mitochondria DNA. The Bayesian phylogenetic tree was constructed using BEAST 2.4. and visualization in Figtree 1.4.4 (tree.bio.ed.ac.uk/software/figtree/). The best model of evolution was carried out using jModelTest 2.1.7. The most optimal was the evolutionary models GTR + I + G with p-inv (I) 0,1990 and gamma shape 0.1960. The main result indicated that the Bali cattle were grouped into Bos javanicus. Phylogenetic analysis also successfully classifying Bos javanicus, Bos indicus, Bos taurus, Bos frontalis and Bos grunniens. These results will complete information about Bali cattle and useful for the preservation and conservation strategies of Indonesian animal genetic resources.

scholarly journals Genetic similarities and phylogenetic analysis of Muntjac (Muntiacus spp.) by comparing the nucleotide sequence of 16S rRNA and cytochrome B genome

2023 ◽  
Vol 83 ◽  
Author(s):  
B. M. Khan ◽  
M. Sabir ◽  
M. N. Alyemeni ◽  
P. Kaushik ◽  
M. Saeed ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Cytochrome B ◽  
Maximum Likelihood Method ◽  
Nucleotide Sequences ◽  
Likelihood Method ◽  
Rrna Gene ◽  
B Genome ◽  
The One

Abstract This study aimed to identify the phylogenetic similarities among the muntjac (Muntiacus spp.). The phylogenetic similarities among seven major muntjac species were studied by comparing the nucleotide sequence of 16s rRNA and cytochrome b genome. Nucleotide sequences, retrieved from NCBI databases were aligned by using DNASTAR software. A phylogenetic tree was created for the selected species of muntjac by using the maximum likelihood method on MEGA7 software. The results of nucleotide sequences (16s rRNA) showed phylogenetic similarities between, the M. truongsonensis and M. rooseveltorum had the highest (99.2%) while the lowest similarities (96.8%) found between M. crinifrons and M. putaoensi. While the results of nucleotide sequences (Cty b) showed the highest similarity (100%) between M. muntjak and M. truongsonensis and the lowest s (91.5%) among M. putaoensis and M. crinifrons. The phylogenetic tree of muntjac species (16s rRNA gene) shows the main two clusters, the one including M. putaoensis, M. truongsonensis, M. rooseveltorum, and M. muntjak, and the second one including M. crinifrons and M. vuquangensis. The M. reevesi exists separately in the phylogenetic tree. The phylogenetic tree of muntjac species using cytochrome b genes shows that the M. muntjak and M. truongsonensis are clustered in the same group.

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

2007 ◽  
Vol 57 (9) ◽  
pp. 2037-2051 ◽  
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.

Caproicibacterium amylolyticum gen. nov., sp. nov., a novel member of the family Oscillospiraceae isolated from pit clay used for making Chinese strong aroma-type liquor

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Yang Gu ◽  
Xiaojun Zhu ◽  
Feng Lin ◽  
Caihong Shen ◽  
Yong Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Novel Genus ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Conserved Genes

An anaerobic, Gram-stain-positive, rod-shaped, motile and spore-forming bacterium, designated strain LBM18003T, was isolated from pit clay used for making Chinese strong aroma-type liquor. Growth occurred at 20–40 °C (optimum, 30–37 °C), pH 4.5–9.5 (optimum, pH 6.5–7.0) and in the presence of 0.0–1.0 % (w/v) sodium chloride (optimum, 0 %). The predominant fatty acids were C16:0, C14:0, C14:0 DMA and C16:0 3-OH, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids and nine unidentified glycolipids. Phylogenetic analysis revealed that strain LBM18003T is a novel member of the family Oscillospiraceae . The 16S rRNA gene sequence similarities of strain LBM18003T to its two most closely related species were less than 94.5 % for distinguishing genera, i.e. closely related to Caproiciproducens galactitolivorans JCM 30532T (94.1 %) and Caproicibacter fermentans DSM 107079T (93.2 %). The genome size of strain LBM18003T was 2 996 201 bp and its DNA G+C content was 48.48 mol%. Strain LBM18003T exhibited 67.8 and 68.1% pairwise-determined whole-genome average nucleotide identity values to Caproiciproducens galactitolivorans JCM 30532T and Caproicibacter fermentans DSM 107079T, respectively; and showed 62.2 and 61.0 % the average amino acid identity values to Caproiciproducens galactitolivorans JCM 30532T and Caproicibacter fermentans DSM 107079T, respectively; and demonstrated 46.1 and 41.5 % conserved genes to Caproiciproducens galactitolivorans JCM 30532T and Caproicibacter fermentans DSM 107079T, respectively. The comparisons of 16S rRNA gene and genome sequences confirmed that strain LBM18003T represented a novel genus of the family Oscillospiraceae . Based on morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic results, strain LBM18003T represents a novel species of a novel genus of the family Oscillospiraceae , for which the name Caproicibacterium amylolyticum gen. nov., sp. nov. is proposed. The type strain is LBM18003T (=GDMCC 1.1626T=JCM 33783T).

Microbacterium paulum sp. nov., isolated from microfiltered milk

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Paolo Bellassi ◽  
Alessandra Fontana ◽  
Maria Luisa Callegari ◽  
Fabrizio Cappa ◽  
Lorenzo Morelli
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Type Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Aerobic ◽  
Species Definition ◽  
Content Type ◽  
Link Type

A novel Gram-stain-positive, strictly aerobic, short rod-shaped bacterium, designated 2CT, was isolated from freshly packaged microfiltered milk. This strain was able to grow within the NaCl concentration range of 0–5 % (w/v), temperature range of 8–37 °C (optimally at 30 °C) and at pH 6.0–10.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2CT was closely related to species of the genus Microbacterium , with the highest sequence similarity (99.2 %) to Microbacterium lacticum DSM 20427T as well as Microbacterium flavum DSM 18909T (=YM18-098T). The phylogenetic tree based on 16S rRNA genes showed that strain 2CT clustered with M. flavum DSM 18909T. However, the phylogenetic tree based on concatenated 16S rRNA and four housekeeping genes showed that strain 2CT clustered with M. lacticum DSM 20427T. Furthermore, the phylogenomic tree showed that strain 2CT clustered with M. lacticum DSM 20427T and M. flavum DSM 18909T. The major respiratory quinones were MK-10, MK-11 and MK-12. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipid composition of strain 2CT consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified glycolipids and two unidentified lipids. The cell-wall peptidoglycan type was a variant of B1α {Gly} [l-Lys] d-Glu-l-Lys, with the amino acids lysine, glycine, alanine and glutamic acid. The whole-cell sugars consisted of galactose, glucose, ribose and minor amounts of rhamnose. In addition, strain 2CT showed a glycolyl-type cell wall. The genomic DNA G+C content was 69.8mol%, while the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the closely related Microbacterium species were below the recognized thresholds of 95–96 % ANI and 70 % DDH for species definition. Based on the phenotypic and genotypic data, strain 2CT (=LMG 32277T=CECT 30329T) is considered to represent a new species, for which the name Microbacterium paulum sp. nov. is proposed.

Paenihalocynthiibacter styelae gen. nov., sp. nov., isolated from stalked sea squirt Styela clava

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Young-Ok Kim ◽  
Jae Koo Noh ◽  
Dong-Gyun Kim ◽  
In-Suk Park ◽  
Sooyeon Park ◽  
...  
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Sea Squirt ◽  
Type Strains

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, MYP1-1T, was isolated from the intestine of a stalked sea squirt (Styela clava) of the South Sea in the Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP1-1T clustered with the type strains of Halocynthiibacter species and Pseudohalocynthiibacter aestuariivivens . Strain MYP1-1T exhibited 16S rRNA gene sequence similarity values of 97.0–97.6 % to the type strains of Halocynthiibacter namhaensis , Halocynthiibacter arcticus and P. aestuariivivens . The phylogenetic tree based on genomic sequences showed that strain MYP1-1T formed a distinct branch separating it from the type strains of two Halocynthiibacter species and P. aestuariivivens and other taxa. The DNA G+C content of strain MYP1-1T from its genomic sequence was 55.0 mol%. Strain MYP1-1T contained Q-10 as the predominant ubiquinone and C18 : 1  ω7c as the major fatty acid. The major polar lipids of strain MYP1-1T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The differences in fatty acid and polar lipid profiles and other differential phenotypic properties made it reasonable to distinguish strain MYP1-1T from the genera Halocynthiibacter and Pseudohalocynthiibacter . On the basis of the polyphasic taxonomic investigations, we conclude that strain MYP1-1T constitutes a new genus and species within the class Alphaproteobacteria , for which the name Paenihalocynthiibacter styelae gen. nov., sp. nov. is proposed. The type strain is MYP1-1T (=KCTC 82143T=NBRC 114355T).

scholarly journals Osteoarticular Infection in Three Young Thoroughbred Horses Caused by a Novel Gram Negative Cocco-Bacillus

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Bernard J. Hudson ◽  
Catherine Chicken ◽  
Anna Blishen ◽  
Kristen H. Todhunter ◽  
Angela P. Begg ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Tree ◽  
Preliminary Analysis ◽  
Causative Organism ◽  
Average Nucleotide Identity ◽  
Kingella Kingae ◽  
Osteoarticular Infection ◽  
Gram Negative ◽  
Thoroughbred Horses ◽  
Low Probability

We describe three cases of osteoarticular infection (OAI) in young thoroughbred horses in which the causative organism was identified by MALDI-TOF as Kingella species. The pattern of OAI resembled that reported with Kingella infection in humans. Analysis by 16S rRNA PCR enabled construction of a phylogenetic tree that placed the isolates closer to Simonsiella and Alysiella species, rather than Kingella species. Average nucleotide identity (ANI) comparison between the new isolate and Kingella kingae and Alysiella crassa however revealed low probability that the new isolate belonged to either of these species. This preliminary analysis suggests the organism isolated is a previously unrecognised species.

Sign in / Sign up

Export Citation Format

Share Document