scholarly journals Cutibacterium modestum and “Propionibacterium humerusii” represent the same species that is commonly misidentified as Cutibacterium acnes

2021 ◽  
Author(s):  
Daniel Goldenberger ◽  
Kirstine K. Søgaard ◽  
Aline Cuénod ◽  
Helena Seth-Smith ◽  
Daniel de Menezes ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Reference Sequence ◽  
Rrna Gene ◽  
Correct Identification ◽  
Skin Microbiome ◽  
Isolation And Identification ◽  
Important Species ◽  
Cutibacterium Acnes ◽  
The 16S Rrna Gene

AbstractCutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was hampered by inconsistent reference data. The isolate was characterised using conventional methods such as Gram stain, MALDI-TOF MS, and antimicrobial susceptibility testing against multiple antimicrobials. Partial 16S rRNA gene sequencing and whole genome sequencing were also performed. In addition, we summarised the available published sequence data and compared prior data to our strain. Conventional phenotypic identification of our isolate resulted in Cutibacterium spp. After analysis of 16S rRNA gene and genome sequences, our isolate was identified as C. modestum, a very recently described species. The 16S rRNA gene analysis was hampered by three incorrect nucleotides within the 16S rRNA gene reference sequence of C. modestum M12T (accession no. LC466959). We also clearly demonstrate that this novel species is identical to tentatively named “Propionibacterium humerusii”. Retrospective data analysis indicates that C. modestum is a clinically important Cutibacterium species often misidentified as C. acnes. The isolation and identification of Cutibacterium spp. is still a challenge. The correct description of very recently named C. modestum and the availability of a correct 16S rRNA sequence of the type strain may help to clarify the taxonomical uncertainty concerning “P. humerusii”. The novel C. modestum is an additional, clinically important species within the genus Cutibacterium and may represent a new member of the human skin microbiome.

scholarly journals Diversity of bacterial communities on the facial skin of different age-group Thai males

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4084 ◽  
Author(s):  
Alisa Wilantho ◽  
Pamornya Deekaew ◽  
Chutika Srisuttiyakorn ◽  
Sissades Tongsima ◽  
Naraporn Somboonna
Keyword(s):  
Young Adults ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
The Us ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene

BackgroundSkin microbiome varies from person to person due to a combination of various factors, including age, biogeography, sex, cosmetics and genetics. Many skin disorders appear to be related to the resident microflora, yet databases of facial skin microbiome of many biogeographies, including Thai, are limited.MethodsMetagenomics derived B-RISA and 16S rRNA gene sequencing was utilized to identify the culture-independent bacterial diversity on Thai male faces (cheek and forehead areas). Skin samples were categorized (grouped) into (i) normal (teenage.hea) and (ii) acne-prone (teenage.acn) young adults, and normal (iii) middle-aged (middle.hea) and (iv) elderly (elderly.hea) adults.ResultsThe 16S rRNA gene sequencing was successful as the sequencing depth had an estimated >98% genus coverage of the true community. The major diversity was found between the young and elderly adults in both cheek and forehead areas, followed by that between normal and acne young adults. Detection of representative characteristics indicated that bacteria from the order Rhizobiales, generaSphingomonasandPseudoalteromonas, distinguished theelderly.heamicrobiota, along the clinical features of wrinkles and pores. Prediction of the metabolic potential revealed reduced metabolic pathways involved in replication and repair, nucleotide metabolism and genetic translation in theelderly.heacompared with that in theteenage.hea. For young adults, some unique compositions such as abundance ofPropionibacterium acnesandStaphylococcus epidermidis, with a minor diversity between normal and acne skins, were detected. The metabolic potentials of the acne vs. normal young adults showed thatteenage.acnwas low in many cellular processes (e.g., cell motility and environmental adaptation), but high in carbohydrate metabolism, which could support acne growth. Moreover, comparison with the age-matched males from the US (Boulder, Colorado) to gain insight into the diversity across national biogeography, revealed differences in the distribution pattern of species, although common bacteria were present in both biogeographical samples. Furthermore, B-RISA served as a crosscheck result to the 16S rRNA gene sequencing (i.e., differences between teenage and elderly microbiota).ConclusionsThis study revealed and compared the microbial diversity on different aged Thai male faces, and included analyses for representing the bacterial flora, the clinical skin characteristics, and comparison with the US age-matched. The results represent the first skin microbiota of Thai males, and helps the design of a large-scale skin microbiome study of Thais. The findings of the diversity among ages, skin type and national biogeography supported the importance of these traits in the skin microbiome and in developing a safe and sustainable treatment for acne and aging skin diseases.

scholarly journals Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks

2018 ◽  
Author(s):  
John S Lambert ◽  
Michael John Cook ◽  
John Eoin Healy ◽  
Ross Murtagh ◽  
Gordana Avramovic ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ixodes Ricinus ◽  
Sanger Sequencing ◽  
Reference Sequence ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Tick Population ◽  
Rrna Gene ◽  
Ixodes Ricinus Ticks ◽  
The 16S Rrna Gene

Lyme borreliosis is a systemic infection caused by tick-borne pathogenic borreliae of the Borrelia burgdorferi sensu lato complex or of the more heterogeneous relapsing fever borrelia group. Clinical distinction of the infections due to different borrelia species is difficult. Accurate knowledge of the prevalence and the species of borreliae in the infected ticks in the endemic areas is valuable for formulating appropriate guidelines for proper management of this infectious disease. The purpose of this research was to design a readily implementable protocol to detect the divergent species of borreliae known to exist in Europe, using Irish samples of Ixodes ricinus ticks as the subject for study. Questing I. ricinus nymph samples were taken at six localities within Ireland. The crude DNA of each dried tick was extracted by hot NH4OH and used to initiate a same-nested PCR with a pair of borrelial genus-specific primers to amplify a highly conserved 357/358 bp segment of the 16S rRNA gene for detection and as the template for Sanger sequencing. To distinguish B. garinii from B. burgdorferi and to discriminate the various strains of B. garinii, a second 282 bp segment of the 16S rRNA gene was amplified for Sanger sequencing. A signature segment of the DNA sequence excised from the computer-generated electropherogram was submitted to the GenBank for BLAST alignment analysis. A 100% ID match with the unique reference sequence in the GenBank was required for the molecular diagnosis of the borrelial species or strain. We found the overall rate of borrelial infection in the Irish tick population to be 5%, with a range from 2% to 12% depending on the locations of tick collection. At least 3 species, namely B. garinii, B. valaisiana and B. miyamotoi, are infecting the ticks collected in Ireland. The isolates of B. garinii were confirmed to be strain BgVir, strain Bernie or strain T25. Since antigens for diagnostic serology tests may be species- or even strain-specific, expanded surveillance of the species and strains of the borreliae among human-biting ticks in Ireland is needed to ensure that the antigens used for the serology tests do contain the epitopes matching the antibodies elicited by the borrelial species and strains in the ticks cohabitating in the same environment.

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).

scholarly journals Diagnosis of Fulminant Pneumonia Caused by Legionella pneumophila Serogroup 8 with the Sequence Analysis of the 16S rRNA Gene

2011 ◽  
Vol 225 (1) ◽  
pp. 65-69 ◽  
Author(s):  
Toshinori Kawanami ◽  
Kazuhiro Yatera ◽  
Kazumasa Fukuda ◽  
Kei Yamasaki ◽  
Masamizu Kunimoto ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Legionella Pneumophila ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

2014 ◽  
Vol 81 (1) ◽  
pp. 48-58 ◽  
Author(s):  
Brandee L. Stone ◽  
Nathan M. Russart ◽  
Robert A. Gaultney ◽  
Angela M. Floden ◽  
Jefferson A. Vaughan ◽  
...  
Keyword(s):  
Lyme Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
North Dakota ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Content Type ◽  
Intergenic Spacer Region ◽  
Grand Forks ◽  
The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

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