scholarly journals Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Ola Alessa ◽  
Yoshitoshi Ogura ◽  
Yoshiko Fujitani ◽  
Hideto Takami ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Phylogenetic Relationship ◽  
Distinct Species ◽  
Genotypic Differences ◽  
Clade C ◽  
Single Genus ◽  
Almost All ◽  
Type Strains ◽  
Dependent Pathway ◽  
Insight Into

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

scholarly journals Phylogeny and differentiation of species of the genus Gluconacetobacter and related taxa based on multilocus sequence analyses of housekeeping genes and reclassification of Acetobacter xylinus subsp. sucrofermentans as Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov.

2010 ◽  
Vol 60 (10) ◽  
pp. 2277-2283 ◽  
Author(s):  
Ilse Cleenwerck ◽  
Paul De Vos ◽  
Luc De Vuyst
Keyword(s):  
Phylogenetic Trees ◽  
Housekeeping Genes ◽  
Distinct Species ◽  
Species Differentiation ◽  
Sequence Analyses ◽  
Phylogenetic Groups ◽  
The Family ◽  
Single Genus ◽  
Reference Strains ◽  
Type Strains

Three housekeeping genes (dnaK, groEL and rpoB) of strains belonging to the genus Gluconacetobacter (37 strains) or related taxa (38 strains) were sequenced. Reference strains of the 15 species of the genus Gluconacetobacter were included. Phylogenetic trees generated using these gene sequences confirmed the existence of two phylogenetic groups within the genus Gluconacetobacter. These groups clustered separately in trees constructed using concatenated sequences of the three genes, indicating that the genus Gluconacetobacter should not remain a single genus and should be split, as suggested previously. Multilocus sequence analysis (MLSA) of the three housekeeping genes also proved useful for species differentiation in the family Acetobacteraceae. It also suggested that Gluconacetobacter xylinus LMG 18788, better known as the type and only strain of Acetobacter xylinus subsp. sucrofermentans, represents a distinct species in the genus Gluconacetobacter, and is not a true G. xylinus strain. In previous studies, this strain showed less than 70 % DNA relatedness to the type strains of G. xylinus and Gluconacetobacter nataicola, the phylogenetically nearest relatives, and could be distinguished from them phenotypically. Additionally, AFLP and (GTG)5-PCR DNA fingerprinting data supported its reclassification within a distinct species. The name Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov. is proposed.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

scholarly journals Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales)

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 422
Author(s):  
Ryosuke Nakai ◽  
Takeshi Naganuma ◽  
Nozomi Tazato ◽  
Tadao Kunihiro ◽  
Sho Morohoshi ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Cellular Fatty Acid ◽  
The Novel ◽  
Nitrogen Gas ◽  
Nitrogen Fixers ◽  
Novel Genus And Species ◽  
Ubiquinone 10 ◽  
Type Strains ◽  
Insight Into

We previously showed that novel filterable bacteria remain in “sterile” (<0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids; and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms.

scholarly journals Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4424-4433 ◽  
Author(s):  
Jakeline Renata Marçon Delamuta ◽  
Renan Augusto Ribeiro ◽  
Ernesto Ormeño-Orrillo ◽  
Marcia Maria Parma ◽  
Itamar Soares Melo ◽  
...  
Keyword(s):  
Environmental Sustainability ◽  
Type Strain ◽  
Housekeeping Genes ◽  
Distinct Species ◽  
Nucleotide Identity ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Tropical Pastures ◽  
Pasture Legumes ◽  
Type Strains

Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).

scholarly journals Therapeutic Exosomes in Prognosis and Developments of Coronary Artery Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Ai-Qun Chen ◽  
Xiao-Fei Gao ◽  
Zhi-Mei Wang ◽  
Feng Wang ◽  
Shuai Luo ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Cell Types ◽  
Biological Functions ◽  
Stent Restenosis ◽  
Artery Disease ◽  
Almost All ◽  
Different Cell Types ◽  
Insight Into ◽  
Systematic Knowledge

Exosomes, with an diameter of 30~150 nm, could be released from almost all types of cells, which contain diverse effective constituent, such as RNAs, proteins, lipids, and so on. In recent years, exosomes have been verified to play an important role in mechanism, diagnosis, treatment, and prognosis of cardiovascular disease, especially coronary artery disease (CAD). Moreover, it has also been shown that exosomes derived from different cell types have various biological functions based on the cell stimulation and microenvironment. However, therapeutic exosomes are currently far away from clinical translation, despite it is full of hope. In this review, we summarize an update of the recent studies and systematic knowledge of therapeutic exosomes in atherosclerosis, myocardial infarction, and in-stent restenosis, which might provide a novel insight into the treatment of CAD and promote the potential clinical application of therapeutic exosomes.

scholarly journals Spiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov.

2020 ◽  
Vol 70 (4) ◽  
pp. 2873-2878 ◽  
Author(s):  
María José León ◽  
Cristina Galisteo ◽  
Antonio Ventosa ◽  
Cristina Sánchez-Porro
Keyword(s):  
Type Species ◽  
Single Species ◽  
Amino Acid Identity ◽  
The Other ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Single Genus ◽  
Type Strains

A comparative taxonomic study of Spiribacter and Halopeptonella species was carried out using a phylogenomic approach based on comparison of the core genome, orthologous average nucleotide identity (OrthoANIu), Genome-to-Genome Distance Calculator (GGDC) and average amino acid identity (AAI). Phylogenomic analysis based on 976 core translated gene sequences obtained from their genomes showed that Spiribacter aquaticus SP30T, S. curvatus UAH-SP71T, S. roseus SSL50T, S. salinus M19-40T and Halopeptonella vilamensis DSM 21056T formed a robust cluster, clearly separated from the remaining species of closely related taxa. AAI between H. vilamensis DSM 21056T and the species of the genus Spiribacter was ≥73.1 %, confirming that all these species belong to the same single genus. On the other hand, S. roseus SSL50T and S. aquaticus SP30T showed percentages of OrthoANIu and digital DNA–DNA hybridization of 98.4 % and 85.3 %, respectively, while these values among those strains and the type strains of the other species of Spiribacter and H. vilamensis DSM 21056T were ≤80.8 and 67.8 %, respectively. Overall, these data show that S. roseus SSL50T and S. aquaticus SP30T constitute a single species and thus that S. aquaticus SP30T should be considered as a later, heterotypic synonym of S. roseus SSL50T based on the rules for priority of names. We propose an emended description of S. roseus , including the features of S. aquaticus . We also propose the reclassification of H. vilamensis as Spiribacter vilamensis comb. nov.

Achondrogenesis

2007 ◽  
Vol 10 (4) ◽  
pp. 253-255 ◽  
Author(s):  
Raj P. Kapur
Keyword(s):  
Cartilage Matrix ◽  
Genotypic Differences ◽  
Skeletal Dysplasias ◽  
Type Ia ◽  
Achondrogenesis Type ◽  
Insight Into ◽  
Developmental Pathology

In this issue of Pediatric and Developmental Pathology, Aigner and colleagues report a detailed investigation of cartilage matrix changes in a 14-week fetus with achondrogenesis type IA [ 1 ]. The changes reported differ from matrix alterations observed in achondrogenesis types IB or II and provide insight into the phenotypic and genotypic differences within this group of skeletal dysplasias.

Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively

2010 ◽  
Vol 60 (4) ◽  
pp. 963-971 ◽  
Author(s):  
Rafael R. de la Haba ◽  
Cristina Sánchez-Porro ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Single Genus ◽  
Type Strains

We have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2–97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA–DNA hybridization between Salinicola socius DSM 19940T, Halomonas salaria DSM 18044T and Chromohalobacter salarius CECT 5903T was 41–21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27T =KCTC 12664T =DSM 18044T) and Salinicola halophilus nom. nov. (type strain CG4.1T =CECT 5903T =LMG 23626T), respectively.

Les Himantariidae ouest-européens, avec la description d’une nouvelle espèce du genre Stigmatogaster Latzel, 1880 (Chilopoda, Geophilomorpha)

2021 ◽  
Vol 126 (2) ◽  
pp. 133-158
Author(s):  
Etienne Iorio
Keyword(s):  
New Species ◽  
European Species ◽  
Identification Keys ◽  
Single Genus ◽  
Western European ◽  
Almost All ◽  
A New Species ◽  
Unpublished Information

The Western-European Himantariidae, with the description of a new species of the genus Stigmatogaster Latzel, 1880 (Chilopoda, Geophilomorpha). After an examination of one or several specimens of almost all of the Western-European species of the genus Stigmatogaster, a new species is described: S. tufi n. sp. apparently endemic to Corsica. New morphological details are given on several Western-European Himantariidae, particularly Stigmatogaster sardoa which is described in detail and confirmed as clearly valid, for some characters of S. excavata and for the female of Himantariella scutellaris which was previously unknown. S. arcisherculis has been again identified in France after 95 years without records in this country. All species so far variously assigned to either Haplophilus or Stigmatogaster are here classified in a single genus Stigmatogaster. Preliminary illustrated identification keys for the Western-European genera of Himantariidae and for the Stigmatogaster species are given also in English. An updated checklist of the Western-European Himantariidae with their distribution is given. Thanks to unpublished information of Lucio Bonato, Himantarium mediterraneum is confirmed in Europe.

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