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1.
Antonie Van Leeuwenhoek ; 116(6): 541-555, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37029880

ABSTRACT

The novel bacterial strain Marseille-P4005T was isolated from the stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod. It grew optimally at 37 °C and at pH 7.0 on 5% sheep blood-enriched Columbia agar after preincubation in a blood-culture bottle supplemented with rumen and blood. This strain does not ferment monosaccharides (except D-tagatose), disaccharides, or polymeric carbohydrates. The major cellular fatty acids were hexadecenoic (24.6%), octadecanoic (22.8%), and tetradecanoic (20.1%) acids. Next-generation sequencing revealed a genome size of 3.2 Mbp with a 56.4 mol% G + C. Phylogenetic analysis based on the 16S rRNA gene highlighted Agathobaculum desmolans strain ATCC 43058T as the closest related strain. The OrthoANI, AAI, and digital DNA-DNA hybridization values were below the critical thresholds of 95%, 95-96%, and 70%, respectively, to define a novel bacterial species. Antibiotic resistance genes APH(3')-IIIa, erm(B), and tet(W) were detected with high identity percentages of 100%, 98.78%, and 97.18% for each gene, respectively. The APH(3')-IIIa gene confers resistance to amikacin, erm(B) gene confers resistance to erythromycin, lincomycin, and clindamycin, while tet(W) gene confers resistance to doxycycline and tetracycline. Based on KEGG BlastKOALA analyses, the annotation results showed that our strain could use glucose to produce L-lactate and pyruvate but not acetate or ethanol. Also, strain Marseille-P4005T was predicted to use phenylalanine to produce indole, a major intercellular signal molecule within the gut microbial ecosystem. Through having a gene coding for tryptophan synthase beta chain (trpB), strain Marseille-P4005T could produce L-tryptophan (an essential amino acid) from indole. Strain Marseille-P4005T showed its highest prevalence in the human gut (34.19%), followed by the reproductive system (17.98%), according to a query carried out on the Integrated Microbial NGS (IMNGS) platform. Based on phylogenetic, phenotypic, and genomic analyses, we classify strain Marseille-P4005T (= CSUR P4005 = CECT 9669), a novel species within the genus Agathobaculum, for which the name of Agathobaculum massiliense sp. nov. is proposed.


Subject(s)
Lactobacillales , Tryptophan , Humans , Tryptophan/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Ecosystem , Kanamycin Kinase/genetics , Base Composition , Genomics , Bacteria/genetics , Lactobacillales/genetics , Fatty Acids/chemistry , Indoles , DNA , DNA, Bacterial/genetics , DNA, Bacterial/chemistry , Sequence Analysis, DNA , Bacterial Typing Techniques
2.
Microbiol Resour Announc ; 12(4): e0125522, 2023 Apr 18.
Article in English | MEDLINE | ID: mdl-36892281

ABSTRACT

Here, we reported two draft genomes of Fusobacterium simiae: strain DSM 19848, initially isolated from monkey dental plaque, and its close relative strain Marseille-Q7035, cultivated from a human intra-abdominal abscess puncture fluid. Their genome sizes are 2.4 Mb and 2.5Mb, respectively. Their G+C contents were 27.1% and 27.2%, respectively.

3.
Int J Mol Sci ; 24(3)2023 Jan 20.
Article in English | MEDLINE | ID: mdl-36768429

ABSTRACT

Brucella intermedia (formerly Ochrobactrum intermedium), a non-fermentative bacterium, has been isolated from animals and human clinical specimens. It is naturally resistant to polymyxins, including colistin (CO), and may cause opportunistic infections in humans. We isolated six Brucella intermedia strains from Senegalese monkey stool. In order to determine whether an efflux pump mechanism was involved in CO resistance in B. intermedia, we evaluated the effects of verapamil (VRP), reserpine (RSP), phe-arg ß-naphthylamide dihydrochloride (PAßN) and carbonyl cyanide 3-chloro phenyl hydrazone (CCCP), four efflux pump inhibitors, on these colistin-resistant strains. Using the broth microdilution method, a CO and CCCP combination of 2 µg/mL and 10 µg/mL, respectively, significantly reduced the CO minimal inhibitory concentration (MIC) of B. intermedia, supporting an efflux pump mechanism. In contrast, VRP, PAßN and RSP did not restore CO susceptibility. A time kill assay showed a bactericidal effect of the CO-CCCP combination. Genomic analysis revealed a potential implication in the CO resistance mechanism of some conserved efflux pumps, such as YejABEF, NorM and EmrAB, as previously reported in other bacteria. An inhibitory effect of the CO-CCCP combination was observed on biofilm formation using the crystal violet method. These results suggest that the intrinsic CO resistance in Brucella intermedia is linked to an efflux pump mechanism and that the synergistic effect of CO-CCCP may open a new field to identify new treatments to restore antibiotic efficacy in humans.


Subject(s)
Brucella , Colistin , Humans , Colistin/pharmacology , Carbonyl Cyanide m-Chlorophenyl Hydrazone/pharmacology , Hydrazones , Anti-Bacterial Agents/pharmacology , Microbial Sensitivity Tests
4.
Arch Microbiol ; 205(1): 3, 2022 Nov 27.
Article in English | MEDLINE | ID: mdl-36436132

ABSTRACT

Strain Marseille-Q6994 was isolated from a 72-year-old patient with pneumonia from Bouches-du-Rhône department, in France. Cells were Gram positive, non-motile, catalase and oxidase-negative cocci. The major fatty acids were hexadecanoic (47.4%) and tetradecanoic acids (28.3%). 16S rRNA gene sequence comparison suggested that strain Marseille-Q6994 was affiliated to the Streptococcus genus. GroEL phylogenetic analysis separated strain Marseille-Q6994 in a distinct branch from the closely related Streptococcus-type strains with standing in nomenclature. Whole genome sequencing-based methods (OrthoAverage Nucleotide Identity, digital DNA-DNA hybridization and pangenome analysis) supported the classification of the strain into a novel species. Therefore, based on the phenotypic, genomic, and phylogenetic analyses, we propose the name Streptococcus bouchesdurhonensis sp. nov for which strain Marseille-Q6994T (CSUR Marseille-Q6994 = DSMZ 113892) is the type strain.


Subject(s)
Genome, Bacterial , Pneumonia , Humans , Aged , RNA, Ribosomal, 16S/genetics , Phylogeny , DNA, Bacterial/genetics , Streptococcus/genetics , Bronchoalveolar Lavage , Pneumonia/genetics
5.
Braz J Microbiol ; 52(3): 1057-1066, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33851342

ABSTRACT

Helicobacter pylori, a human pathogen that colonizes the stomach of 50% of the world's population, is associated with gastritis, gastric adenocarcinoma, and mucosa-associated lymphoid tissue (MALT) lymphoma. Diseases are characterized by severe inflammatory responses in the stomach that are induced by various chemokines and cytokines. Recently, oncostatin M (OSM), an IL-6 family cytokine, was detected in early gastric cancer biopsies. In this study, we showed that Helicobacter pylori induced secretion of OSM and overexpression of its type II receptor OSMRß (OSM/OSMRß) in a human gastric adenocarcinoma cell line (AGS) over 24 h of infection. Furthermore, we showed that the induction of OSM and OSMRß was carried out by heat-sensitive Helicobacter pylori outer membrane vesicle (OMV) protein. Collectively, our results established, for the first time, a direct relation between Helicobacter pylori OMVs and the OSM/OSMRß signaling axis.


Subject(s)
Adenocarcinoma , Bacterial Outer Membrane , Helicobacter Infections , Oncostatin M , Stomach Neoplasms , Adenocarcinoma/metabolism , Gastric Mucosa , Helicobacter Infections/metabolism , Helicobacter pylori/genetics , Humans , Oncostatin M/metabolism , Oncostatin M Receptor beta Subunit/metabolism , Signal Transduction , Stomach Neoplasms/metabolism
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