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Microbial Ecology May 2023Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt...
Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.
Topics: Animals; Humans; Trichomonas; Eagles; Europe
PubMed: 35385973
DOI: 10.1007/s00248-022-02002-y -
International Journal of Systematic and... Aug 2021Two rod-shaped and Gram-stain-positive bacteria (strains C64 and C62) were isolated in 2020 from faeces of greater white-fronted geese () from Poyang Lake, PR China....
Two rod-shaped and Gram-stain-positive bacteria (strains C64 and C62) were isolated in 2020 from faeces of greater white-fronted geese () from Poyang Lake, PR China. Their optimal growth conditions were at 37 °C, pH 7.0 and with 0.5 % (w/v) NaCl. The two isolates showed a highest 16S rRNA gene sequence similarity to DSM 19116 (92.1 %). Phylogenetic/phylogenomic analyses indicated that strains C64 and C62 clustered independently in the vicinity of the genera , and within the family , but could not be classified clearly as members of any of these known genera. The average amino acid identity values between our isolates and available genomes of members of the family were around the genus threshold value (45-65 %). The major cellular fatty acids of the strains were Cω and C. The predominant polar lipids were phosphatidylinositol, phosphatidylglycerol, phosphatidylcholine, diacylglycerol, triacylglycerol and cardiolipin. The amino acid composition of peptidoglycan contained alanine, glutamic acid and glycine. The major respiratory menaquinones were MK-8(H) and MK-9(H). The whole cell sugars included galactose, arabinose and glucose. On the basis of the results of the 16S rRNA gene sequences comparison, whole-genome phylogenomic analysis, phenotypic and chemotaxonomic characteristics, we propose that strains C64 and C62 represent a novel species belonging to a novel genus within the family , for which the name gen. nov., sp. nov. is proposed. The type strain is C64 (=CGMCC 1.18410=GDMCC 1.1969=KCTC 49511=KACC 22143).
Topics: Actinomycetaceae; Animals; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Feces; Geese; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2
PubMed: 34431769
DOI: 10.1099/ijsem.0.004978 -
New Microbes and New Infections Nov 2019sp. nov. strain Marseille-P2802 (= CSUR P2802 = DSM 103074) is a new species within the genus in the phylum Actinobacteria that was isolated from the urine of a...
sp. nov. strain Marseille-P2802 (= CSUR P2802 = DSM 103074) is a new species within the genus in the phylum Actinobacteria that was isolated from the urine of a 59-year-old man treated with chronic haemodialysis for diabetic nephropathy.
PubMed: 31641508
DOI: 10.1016/j.nmni.2019.100591 -
New Microbes and New Infections Sep 2019Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight...
Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: sp. nov. strain Marseille-P5647, sp. nov. strain Marseille-P5644 and sp. nov. strain Marseille-P5995, which we describe according to the concept of taxonogenomics.
PubMed: 31367386
DOI: 10.1016/j.nmni.2019.100585 -
New Microbes and New Infections Sep 2019sp. nov. strain Marseille-P3369 (= CSURP3369) is a new species from the order that has been isolated from a fresh stool sample of a healthy French woman.
sp. nov. strain Marseille-P3369 (= CSURP3369) is a new species from the order that has been isolated from a fresh stool sample of a healthy French woman.
PubMed: 31333849
DOI: 10.1016/j.nmni.2019.100575 -
New Microbes and New Infections Jul 2017Here we report the main characteristics of sp. nov., CSUR-P3385 and sp. nov., CSUR-P3369 isolated in September 2016 from a fresh stool sample of healthy French...
Here we report the main characteristics of sp. nov., CSUR-P3385 and sp. nov., CSUR-P3369 isolated in September 2016 from a fresh stool sample of healthy French volunteer woman.
PubMed: 28480042
DOI: 10.1016/j.nmni.2017.03.002 -
Journal of Global Antimicrobial... Mar 2017Patterns of antimicrobial susceptibility in Actinomyces and related genera are very limited in the literature. Data of predominant susceptibility profiles could...
OBJECTIVES
Patterns of antimicrobial susceptibility in Actinomyces and related genera are very limited in the literature. Data of predominant susceptibility profiles could contribute to the establishment of an accurate empirical treatment.
METHODS
A total of 113 isolates from clinical samples were included in this study. Each isolate was identified using phenotypic methods and MALDI-TOF/MS. When discrepancies were observed, 16S rRNA gene sequencing was performed. The minimum inhibitory concentrations (MICs) of nine antimicrobial agents (penicillin, ceftriaxone, linezolid, tetracycline, clindamycin, erythromycin, ciprofloxacin, levofloxacin and vancomycin) were tested against the species Actinotignum schaalii (n=23), Actinomyces turicensis (n=18), Actinomyces europaeus (n=13), Actinomyces naeslundii/Actinomyces viscosus group (n=12), Actinomyces urogenitalis (n=11), Actinomyces radingae (n=11), Actinomyces neuii (n=9), Actinomyces odontolyticus (n=8), Bifidobacterium scardovii (n=3), Actinomyces graevenitzii (n=2), Alloscardovia omnicolens (n=2) and Varibaculum cambriense (n=1).
RESULTS
All of the isolates were susceptible to penicillin, ceftriaxone, vancomycin and linezolid. Almost all of the A. urogenitalis isolates (8/11) were resistant to clindamycin and showed susceptibility to erythromycin, suggesting an L-phenotype, however no determinants of clindamycin resistance (lnu and lsa genes) were detected by PCR. High MIC values to quinolones were observed in 54/113 isolates (47.8%). All of the A. urogenitalis isolates were highly resistant to ciprofloxacin and levofloxacin.
CONCLUSIONS
These data highlight the importance of ongoing surveillance to provide relevant information for empirical management of infections caused by these organisms.
Topics: Actinobacteria; Actinomycosis; Anti-Bacterial Agents; Bacteriological Techniques; Clindamycin; DNA, Bacterial; DNA, Ribosomal; Drug Resistance, Bacterial; Humans; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 28109846
DOI: 10.1016/j.jgar.2016.11.007 -
Systematic and Applied Microbiology Dec 2016During the years 1994-2011 five strictly anaerobic, Gram-stain-positive, diphtheroid bacteria (strains CCUG 31793, CCUG 44221, CCUG 61255, CCUG 45114, and CCUG 44993)...
During the years 1994-2011 five strictly anaerobic, Gram-stain-positive, diphtheroid bacteria (strains CCUG 31793, CCUG 44221, CCUG 61255, CCUG 45114, and CCUG 44993) were isolated from different clinical samples in Sweden and the United Kingdom. Comparative analysis of 16S rRNA gene sequences showed that the five strains shared 99-100% 16S rRNA gene sequence similarity among each other and 98.3-98.6% sequence similarity to Varibaculum cambriense DSM 15806. Genomic fingerprint patterns generated with ERIC-, BOX-, and RAPD-PCR, and whole genome sequence (WGS) based comparison by in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) analysis and six housekeeping gene (atpA, rpoB, pgi, metG, gltA and gyrA) based multilocus sequence analysis (MLSA) showed that the strains could be differentiated from V. cambriense DSM 15806 and formed three genomic groups, which could only be differentiated at the species border level. Based on physiological characterizations the five strains could not be clearly distinguished among each other. Based on those data a new Varibaculum species, Varibaculum anthropi (type strain CCUG 31793=JCM 19104) is proposed including three genetically distinct genomovars (gv 1: CCUG 31793, CCUG 44221, CCUG 61255; gv 2: CCUG 45114, and gv 3: CCUG 44993).
Topics: Actinomycetaceae; Adolescent; Adult; Base Sequence; DNA, Bacterial; Female; Genome, Bacterial; Humans; Male; Middle Aged; Multilocus Sequence Typing; Nucleic Acid Hybridization; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 27745752
DOI: 10.1016/j.syapm.2016.09.002 -
New Microbes and New Infections Sep 2016We report the main characteristics of "Varibaculum massiliense" strain Marseille-P2802(T) (=CSUR P2802), which was isolated from urine sample of a 59-year-old man with...
We report the main characteristics of "Varibaculum massiliense" strain Marseille-P2802(T) (=CSUR P2802), which was isolated from urine sample of a 59-year-old man with end-stage renal disease.
PubMed: 27504187
DOI: 10.1016/j.nmni.2016.06.011