Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov.

Lawson, Paul A.; Patel, Niyati; Mohammed, Ahmed Dawood; Moore, Edward R. B.; Lo, Alexander S; Sardi, Armando; Davis, Joel L.; Doyle, D. Annie; Hui, Yvonne; Testerman, Traci L.

doi:10.1099/ijsem.0.004204

Cited by 17 publications

(4 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Even though chemotaxonomic procedures marked a turning point in prokaryotic systematics (Goodfellow et al, 2012), results can be influenced by cultivation conditions (i.e., fatty acid analysis) or by inexperienced staff (i.e., regarding the interpretation of polar lipids patterns on 2-D TLC plates; Sutcliffe et al, 2013). In favour of a revitalization of bacterial taxonomy, in silico chemotaxonomic analyses were already used in some studies to complement and, in some cases, replace characteristics traditionally determined in the laboratory (Amaral et al, 2014;Fotedar et al, 2020;10.3389/fmicb.2022.975365 Frontiers in Microbiology 13 frontiersin.org Lawson et al, 2020). Here, we attempted to determine in silico cell-wall peptidoglycan, respiratory quinone, fatty acids and polar lipid patterns of Geodermatophilaceae.…”

Section: Final Remarks and Taxonomic Consequencesmentioning

confidence: 99%

“…Laboratory-based DNA–DNA hybridisation methods have already been routinely replaced by overall genome relatedness indices (OGRI; Chun et al, 2018 ) of which digital DNA:DNA hybridization was shown to be the best-performing method ( Meier-Kolthoff et al, 2013a ). The use of in silico analysis for chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory ( Amaral et al, 2014 ; Fotedar et al, 2020 ; Lawson et al, 2020 ) with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports ( Chun and Rainey, 2014 ; Whitman, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genotype–phenotype correlations within the Geodermatophilaceae

et al. 2022

View full text Add to dashboard Cite

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype–phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.

show abstract

Section: Final Remarks and Taxonomic Consequencesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genotype–phenotype correlations within the Geodermatophilaceae

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Members of this family are Gramstain-negative, usually non-motile, rod-shaped, aerobic or facultative anaerobic and contain MK-7 as the predominant respiratory ubiquinone [1][2][3][4][5][6]. At the time of writing, the family Chitinophagaceae was composed of 44 genera with validly published names (https://lpsn.dsmz.de/family/chitinophagaceae) and was supplemented with Agriterribacter [2], Parapseudoflavitalea [3], Limnovirga [4], Phnomibacter [5] and Pinibacter [6] in the past 2 years. Species in this family usually possess various functions in the environment [7][8][9][10][11][12][13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

“…The family Chitinophagaceae , belonging to the phylum Bacteroidota, was proposed by Kämpfer et al [1] and incorporated several genera on the basis of 16S rRNA gene sequence analyses and some phenotypic similarities. Members of this family are Gram-stain-negative, usually non-motile, rod-shaped, aerobic or facultative anaerobic and contain MK-7 as the predominant respiratory ubiquinone [1–6]. At the time of writing, the family Chitinophagaceae was composed of 44 genera with validly published names (https://lpsn.dsmz.de/family/chitinophagaceae) and was supplemented with Agriterribacter [2], Parapseudoflavitalea [3], Limnovirga [4], Phnomibacter [5] and Pinibacter [6] in the past 2 years.…”

Section: Introductionmentioning

confidence: 99%

Agriterribacter soli sp. nov., isolated from herbicide-contaminated soil

Song

Mao

Liu

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

A Gram-stain-negative, non-spore-forming and rod-shaped bacterium, designated strain NS-102T, was isolated from herbicide-contaminated soil sampled in Nanjing, PR China, and its taxonomic status was investigated by a polyphasic approach. Cell growth of strain NS-102T occurred at 16–42 °C (optimum, 30 °C), at pH 5.0–8.0 (optimum, pH 6.0) and in the presence of 0–3.5 % (w/v) NaCl (optimum, without addition of NaCl). The 16S rRNA gene sequence of strain NS-102T shows high similarity to that of Agriterribacter humi YJ03T (96.9 % similarity), followed by Terrimonas terrae T16R-129T (93.8 %) and Terrimonas pekingensis QHT (93.6 %). Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the draft genomes of strain NS-102T and A. humi YJ03T were 72.5, 69.4 and 18.6%, respectively. The only respiratory quinone was MK-7, and phosphatidylethanolamine and unidentified lipids were the major polar lipids. The major cellular fatty acids of strain NS-102T contained high amounts of iso-C15 : 0 (24.6 %), iso-C17 : 03-OH (24.1 %), iso-C15 : 0 G (16.6 %) and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) (15.6 %). The G+C content of the total DNA was determined to be 40.0 mol%. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain NS-102T represents a novel species of the genus Agriterribacter , for which the name Agriterribacter soli sp. nov. is proposed. The type strain is NS-102T (=CCTCC AB 2017249T=KCTC 62322T).

show abstract