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1.
Dig Dis Sci ; 68(9): 3557-3561, 2023 09.
Article in English | MEDLINE | ID: mdl-37402980

ABSTRACT

BACKGROUND: Evidence suggests that upregulation of tumor necrosis factor-alpha (TNF-α) plays a role in immune dysregulation in both preeclampsia and inflammatory bowel disease (IBD). AIMS: We aimed to investigate whether anti-TNF therapy during pregnancy decreases the risk of preeclampsia in women with IBD. METHODS: The study population included women with IBD and pregnancies who were followed at a tertiary care center from 2007 to 2021. Cases of preeclampsia were compared with controls with a normotensive pregnancy. Data on patient demographics, disease type and activity, pregnancy complications, and additional risk factors for preeclampsia were collected. The association between anti-TNF therapy and preeclampsia was analyzed using univariate analysis and multivariate logistic regression. RESULTS: Women with preeclampsia were more likely to have a preterm delivery (44% vs. 12%, p < 0.001). More women without preeclampsia were exposed to anti-TNF therapy during pregnancy than women with preeclampsia (55% vs. 30%, p = 0.029). The majority of women (32/44) on anti-TNF therapy, either adalimumab or infliximab, continued to have some degree of exposure during the third trimester. Though not significant, multivariate analysis showed a trend towards a protective effect of anti-TNF therapy against developing preeclampsia if exposed during the third trimester (OR 0.39; 95% CI 0.14-1.12, p = 0.08). CONCLUSIONS: In this study, anti-TNF therapy exposure was higher in IBD patients who did not develop preeclampsia than in those who did. While not significant, there was a trend towards a protective effect of anti-TNF therapy against preeclampsia if exposed during the third trimester.


Subject(s)
Inflammatory Bowel Diseases , Pre-Eclampsia , Pregnancy , Infant, Newborn , Humans , Female , Pre-Eclampsia/epidemiology , Tumor Necrosis Factor Inhibitors/adverse effects , Inflammatory Bowel Diseases/complications , Inflammatory Bowel Diseases/drug therapy , Infliximab/adverse effects , Adalimumab/adverse effects , Tumor Necrosis Factor-alpha , Necrosis
2.
Int J Syst Evol Microbiol ; 70(11): 5676-5685, 2020 Nov.
Article in English | MEDLINE | ID: mdl-32931407

ABSTRACT

Nine Gram-stain-positive cocci, coccobacilli or short, rod-shaped strains recovered from clinical sources from patients located in two Canadian provinces and one environmental source were extensively studied. Clinical sources included blood cultures, cerebral spinal fluid, lymph node, lung biopsy and peritoneal fluid. Through 16S rRNA gene and whole genome sequencing analyses, the strains were found to cluster into three groups, closest to but distinguished from other genera in the family Propionibacteriaceae. The genomes from these bacteria had high G+C content, ranging from 67.8-69.56 mol%, and genome sizes of 3.02-4.52 Mb. Biochemical and chemotaxonomic properties including branched-chain cellular fatty acids, l-lysine diaminopimelic acid (ll-DAP) and cell-wall type A3γ (ll-DAP-gly) containing ll-DAP, alanine, glycine and glutamic acid were found and so the strains were therefore deemed to be consistent with other new genera in this family. Based on this investigation, we propose Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov. for these taxa. Misidentified taxon 'Ponticoccus gilvus' was found to be assignable to Enemella evansiae based on this study.


Subject(s)
Body Fluids/microbiology , Phylogeny , Propionibacteriaceae/classification , Bacterial Typing Techniques , Base Composition , Canada , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Genome Size , Genome, Bacterial , Humans , Propionibacteriaceae/isolation & purification , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
3.
Int J Syst Evol Microbiol ; 70(6): 3639-3646, 2020 Jun.
Article in English | MEDLINE | ID: mdl-32501783

ABSTRACT

A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191FT, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family Chitinophagaceae that was distinct from members of the genus Pseudoflavitalea (95.1-95.2 % sequence similarity) and Pseudobacter ginsenosidimutans (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191FT and Pseudoflavitalea rhizosphaerae T16R-265T and Pseudobacter ginsenosidimutans Gsoil 221T was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191FT was MK-7 and the major fatty acids were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191FT calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191FT represents a novel species and genus for which the name Parapseudoflavitalea muciniphila gen. nov., sp. nov. is proposed. The type strain is PMP191FT (=DSM 104999T=ATCC BAA-2857T = CCUG 72691T). The phylogenetic analyses also revealed that Pseudobacter ginsenosidimutans shared over 98 % sequence similarly to members of the genus Pseudoflavitalea. However, the average nucleotide identity value between Pseudoflavitalea rhizosphaerae T16R-265T, the type species of the genus and Pseudobacter ginsenosidimutans Gsoil 221T was 86.8 %. Therefore, we also propose that Pseudobacter ginsenosidimutans be reclassified as Pseudoflavitalea ginsenosidimutans comb. nov.


Subject(s)
Bacteroidetes/classification , Peritoneal Neoplasms/microbiology , Phylogeny , Bacterial Typing Techniques , Bacteroidetes/isolation & purification , Baltimore , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Glycolipids/chemistry , Humans , Phosphatidylethanolamines/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
4.
Int J Syst Evol Microbiol ; 69(4): 1142-1148, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30767850

ABSTRACT

A novel Gram-stain-positive, non-motile, non-spore-forming coccus-shaped obligately anaerobic bacterium was recovered from a fecal sample obtained from an individual from a traditional community located on the southern coast of Peru. The results of analysis based on 16S rRNA gene sequencing indicated the novel bacterium to be phylogenetically distinct from other genera of members of the Peptoniphilaceae family, sharing a loose affinity with the genera Ezakiella, Finegoldia, Gallicola and Parvimonas. The major cellular fatty acids of the novel isolate were determined to be C16:0, C17:1ω8c, and C18:1ω9c. The DNA G+C content was 29.9 mol%. End products of metabolism from peptone yeast glucose broth (PYG) were determined to be acetate and methyl succinate. The diagnostic diamino acid present in the cell wall was lysine. On the basis of the phenotypic, chemotaxonomic and phylogenetic results the organism is a member of a novel genus belonging to the family Peptoniphilaceae for which the name Citroniella saccharovorans gen nov. sp. nov., is proposed. The type strain is M6.X9T (DSM 29873T=CCUG 66799T).


Subject(s)
Clostridiales/classification , Feces/microbiology , Phylogeny , Bacterial Typing Techniques , Base Composition , Clostridiales/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Humans , Peru , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
5.
Int J Syst Evol Microbiol ; 69(1): 235-240, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30484761

ABSTRACT

A novel Gram-stain-negative, rod-shaped, motile, non-spore-forming, facultatively anaerobic marine bacterium was isolated from the gastrointestinal tract of the sandworm Alitta succinea collected from Grice Cove, South Carolina, USA. The strain was arginine dihydrolase-positive, and oxidase- and catalase-positive. Growth occurred between 10 and 37 °C, with optimal growth occurring between 30 and 32 °C. Comparative 16S rRNA gene sequence analysis showed its nearest neighbours are members of the genus Kistimonas of the family Hahellaceae, which is found in the order Oceanospirillales, class Gammaproteobacteria. The closest related species was Kistimonas asteriae KMD 001T with 16S rRNA gene sequence similarity of 99.0 %. However, DNA-DNA hybridization between these strains revealed less than 70 % DNA-DNA relatedness, supporting the novel species status of the strain. The major fatty acids were C16 : 0, C18 : 0, C18 : 1ω7c and a summed feature that contained C16 : 1ω6c/C16 : 1ω7c. The major respiratory quinone was ubiquinone-9 and the predominant polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 52.5 mol%. Based on the data presented, strain BGP-2T is considered to represent a novel member of the genus Kistimonas, for which the name Kistimonas alittae sp. nov. is proposed. The type strain is BGP-2T (=CCUG 65711T=JCM 30010T).


Subject(s)
Gammaproteobacteria/classification , Gastrointestinal Tract/microbiology , Phylogeny , Polychaeta/microbiology , Animals , Aquatic Organisms/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Gammaproteobacteria/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , South Carolina , Ubiquinone/chemistry
6.
Int J Syst Evol Microbiol ; 68(4): 1052-1058, 2018 Apr.
Article in English | MEDLINE | ID: mdl-29458489

ABSTRACT

A cultivation-based study of the microbial diversity of cellular phone screens led to the isolation of a Gram-stain-positive, aerobic, rod-shaped and non-endospore-forming bacterium, designated S2T63T, exhibiting phenotypic and genotypic characteristics unique to the type strains of closely related species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is a member of Microbacterium, and most closely related to Microbacterium aurantiacum IFO 15234T and Microbacterium kitamiense Kitami C2T. The DNA-DNA relatedness values of the strain S2T63T to M. aurantiacum KACC 20510T, M. kitamiense KACC 20514Tand Microbacterium laevaniformans KACC 14463T were 65 % (±4), 29.5 % (±3) and 55.9 % (±4), respectively. The genomic DNA G+C content was 71.8 mol%. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified polar lipids. The peptidoglycan contained the amino acids glycine, lysine, alanine and glutamic acid, with substantial amounts of hydroxy glutamic acid detected, which is characteristic of peptidoglycan type B1α. The predominant menaquinones were MK-12 and MK-13. Rhamnose, fucose and galactose were the whole-cell sugars detected. The strain also showed biofilm production, estimated by using crystal violet assay. Based on the results of the phenotypic and genotypic characterizations, it was concluded that the new strain represents a novel species of the genus Microbacterium, for which the name Microbacteriumtelephonicum is proposed, with S2T63T (=MCC 2967T=KACC 18715T=LMG 29293T) as the type strain.


Subject(s)
Actinomycetales/classification , Cell Phone , Phylogeny , Actinomycetales/genetics , Actinomycetales/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Nucleic Acid Hybridization , Peptidoglycan/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/chemistry
7.
Int J Syst Evol Microbiol ; 67(10): 4132-4145, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28905708

ABSTRACT

The proteolytic bacterium strain A7P-90mT was isolated from Lake Untersee, Antarctica. The anoxic water was collected from a perennially sealed (~100 millennia) glacial ice lake. Gram-stain-negative cells were 0.18-0.3×8.0-25.0 µm in size, straight, slender rods with unusual gliding motility by external, not previously reported, organelles named here as antiae. At the end of stationary phase of growth, spheroplasts were terminally formed and the cells resembled dandelions. After death, cells were helical. The isolate was an athalassic, strictly anaerobic and catalase-negative proteolytic chemoorganotroph. It was moderately psychrophilic with a temperature range for growth of 3-26 °C and an optimum at 22-23 °C. The pH range for growth was 5.5-7.8 with an optimum at 6.9. Major cellular fatty acids were branched pentadecanoic and tridecanoic acids, and saturated tetradecanoic acids. The quinone system comprised menaquinone MK-7. The strain was sensitive to all checked antibiotics and ascorbic acid. The G+C content of the genomic DNA was 42.6 mol%. Based on average nucleotide identity, average amino acid identity and phylogenetic analyses, the novel isolate was placed within a unique phylogenetic cluster distant from all eight families in the order Bacteroidales and formed a novel family with the proposed name Williamwhitmaniaceae fam. nov. The description of the order Bacteroidales was emended accordingly. The name Williamwhitmania taraxaci gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain A7P-90mT (=DSM 100563T=JCM 30888T). The complete draft genome sequence was deposited at the Joint Genomes Institute (JGI) under number IMG OID 2654588148 and in SRA listed as SRP088197.


Subject(s)
Bacteroidetes/classification , Lakes/microbiology , Phylogeny , Antarctic Regions , Bacterial Typing Techniques , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
8.
Int J Syst Evol Microbiol ; 67(5): 1442-1450, 2017 May.
Article in English | MEDLINE | ID: mdl-28150571

ABSTRACT

A novel psychrotolerant bacterium, strain ISLP-3T, was isolated from a sample of naturally formed ice sculpture on the shore of Lake Podprudnoye in Antarctica. Cells were motile, stained Gram-positive, non-spore-forming, straight or slightly curved rods with the shape of a baseball bat. The new isolate was facultatively anaerobic and catalase-positive. Growth occurred at 3-35 °C with an optimum at 22-24 °C, 0-2 % (w/v) NaCl with an optimum at 0.3 % and pH 6.2-9.5 with an optimum at pH 7.5. Strain ISLP-3T grew on several carbon sources, with the best growth on cellobiose. The isolate possessed ureolytic activity but growth was inhibited by urea. The strain was sensitive to: ampicillin, gentamycin, kanamycin rifampicin, tetracycline and chloramphenicol. Major fatty acids were: anteiso-C15 : 0, iso-C16 : 0, C16 : 0, C14 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H4). The genomic G+C content was 69.5 mol%. The 16S rRNA gene showed 99 % sequence similarity to that of Sanguibacter suarezii ST-26T, but their recA genes shared ≤91 % sequence similarity, suggesting that this new isolate represents a novel species within the genus Sanguibacter. This conclusion was supported by average nucleotide identity, which was ≤91 % to the most closely related strain. The name Sanguibacter gelidistatuariae sp. nov. is proposed for the novel species with the type strain ISLP-3T=ATCC TSD-17T=DSM 100501T=JCM 30887T). The complete genome draft sequence of ISLP-3T was deposited under IMG OID 2657245272. Emendments to the descriptions of related taxa have been made based on experimental data from our comparative analysis.


Subject(s)
Actinomycetales/classification , Ice , Phylogeny , Actinomycetales/genetics , Actinomycetales/isolation & purification , Antarctic Regions , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , RNA, Ribosomal, 16S/genetics , Sculpture , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
9.
Int J Syst Evol Microbiol ; 67(5): 1247-1254, 2017 05.
Article in English | MEDLINE | ID: mdl-28100298

ABSTRACT

To better characterize murine intestinal microbiota, a large number (187) of Gram-positive-staining, rod- and coccoid-shaped, and facultatively or strictly anaerobic bacteria were isolated from small and large intestinal contents from mice. Based on 16S rRNA gene sequencing, a total 115 isolates formed three phylogenetically distinct clusters located within the family Erysipelotrichaceae. Group 1, as represented by strain NYU-BL-A3T, was most closely related to Allobaculum stercoricanis, with 16S rRNA gene sequence similarity values of 87.7 %. A second group, represented by NYU-BL-A4T, was most closely related to Faecalibaculum rodentium, with 86.6 % 16S rRNA gene sequence similarity. A third group had a nearly identical 16S rRNA gene sequence (99.9 %) compared with the recently described Faecalibaculum rodentium, also recovered from a laboratory mouse; however, this strain had a few differences in biochemical characteristics, which are detailed in an emended description. The predominant (>10 %) cellular fatty acids of strain NYU-BL-A3T were C16 : 0 and C18 : 0, and those of strain NYU-BL-A4T were C10 : 0, C16 : 0, C18 : 0 and C18 : 1ω9c. The two groups could also be distinguished by multiple biochemical reactions, with the group represented by NYU-BL-A4T being considerably more active. Based on phylogenetic, biochemical and chemotaxonomic criteria, two novel genera are proposed, Ileibacterium valens gen. nov., sp. nov. with NYU-BL-A3T (=ATCC TSD-63T=DSM 103668T) as the type strain and Dubosiella newyorkensis gen. nov., sp. nov. with NYU-BL-A4T (=ATCC TSD-64T=DSM 103457T) as the type strain.


Subject(s)
Faecalibacterium/classification , Intestines/microbiology , Mice/microbiology , Phylogeny , Tenericutes/classification , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tenericutes/genetics , Tenericutes/isolation & purification
10.
Int J Syst Evol Microbiol ; 66(9): 3393-3399, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27259292

ABSTRACT

A polyphasic taxonomic study was performed on two Gram-positive-staining, anaerobic, pleomorphic, rod-shaped strains isolated from human bone and tissue samples. Sequencing of the 16S rRNA genes revealed that the strains belong to a novel species within the genus Propionibacterium, most closely related to Propionibacterium acnes subsp. acnes and Propionibacterium acnes subsp. elongatum with similarity values of 98.4 % and 98.1 %, respectively. In addition, protein-coding genes for rpoB, recA and gyrB clearly separated the novel organism from all species and subspecies of the genus Propionibacterium. However, a DNA-DNA hybridization analysis between the novel organism and the type strain P. acnes ATCC 6919T revealed a value of only 61.1 %. Furthermore, whole genome analysis using the program OrthoANI gave a value of 88.5 %, which is significantly below the cut-off value of 95 % for species delineation. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0. The DNA G+C content of the type strain was 59.7 mol%. When taken collectively, phenotypic, molecular genetic, chemotaxonomic and phylogenetic information demonstrate that the organism represents a distinct, albeit close relative of P. acnes On the basis of the results presented, the organism represents a novel member of the genus Propionibacterium for which the name Propionibacterium namnetense sp. nov. is proposed. The type strain is NTS 31307302T (=DSM 29427T=CCUG 66358T).


Subject(s)
Bone Diseases, Infectious/microbiology , Phylogeny , Propionibacterium/classification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , France , Humans , Male , Nucleic Acid Hybridization , Propionibacterium/genetics , Propionibacterium/isolation & purification , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Young Adult
11.
Int J Syst Evol Microbiol ; 66(8): 2929-2935, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27130323

ABSTRACT

Gram-stain-positive, partially acid-fast, non-spore-forming, anaerobic, catalase-positive, pleomorphic bacteria were isolated from human abscesses. Strains X1036T, X1698 and NML 120705, were recovered from a spinal abscess, a peritoneal abscess and a breast abscess respectively. A phylogenetic analysis of the 16S rRNA gene sequences showed that the strains shared 100 % similarity, and the nearest phylogenetic neighbour was Dietzia timorensis DSM 45568T (95%). Chemotaxonomic characteristics of the strains were consistent with those described for members of the suborder Corynebacterineae. Mycolic acids were detected using HPLC and one-dimensional TLC; whole-cell hydrolysates yielded meso-diaminopimelic acid with arabinose and galactose as the predominant sugars; the muramic acid acyl type was acetylated; the major menaquinone was MK-9 (96.3%); polar lipids detected were phosphatidylglycerol, phosphatidylinositol and an unknown glycophospholipid. Cellular fatty acids were hexadecanoic acid (C16 : 0), octadecenoic acid (C18 : 1ω9c) and decanoic acid (C10 : 0). Tuberculostearic acid was not detected. Based on the results of this polyphasic study, we conclude that these strains represent a novel genus and species within the suborder Corynebacterineae for which we propose the name Lawsonella clevelandensis gen. nov., sp. nov., with the type strain X1036T (=DSM 45743T=CCUG 66657T).


Subject(s)
Abscess/microbiology , Actinobacteria/classification , Phylogeny , Actinobacteria/genetics , Actinobacteria/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Humans , Male , Middle Aged , Muramic Acids/chemistry , Mycolic Acids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spine/microbiology , Spine/pathology
12.
Int J Syst Evol Microbiol ; 66(5): 2019-2024, 2016 May.
Article in English | MEDLINE | ID: mdl-26907921

ABSTRACT

A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T).


Subject(s)
Feces/microbiology , Firmicutes/classification , Gram-Positive Cocci/classification , Phylogeny , Bacteria, Anaerobic/classification , Bacteria, Anaerobic/genetics , Bacteria, Anaerobic/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Firmicutes/genetics , Firmicutes/isolation & purification , Gram-Positive Cocci/genetics , Gram-Positive Cocci/isolation & purification , Humans , Peru , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
13.
Int J Syst Evol Microbiol ; 66(12): 5529-5536, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27902285

ABSTRACT

A Gram-stain-positive bacterium, strain LZ-22T, was isolated from a rhizosphere of moss Leptobryum sp. collected at the shore of Lake Zub in Antarctica. Cells were motile, straight or pleomorphic rods with sizes of 0.6-1.0×3.5-10 µm. The novel isolate was a facultatively anaerobic, catalase-positive, psychrotolerant mesophile. Growth was observed at 3-41 °C (optimum 24-28 °C), with 0-7 % (w/v) NaCl (optimum 0.25 %) and at pH 4.0-9.0 (optimum pH 7.8). The quinone system of strain LZ-22T possessed predominately menaquinone MK-9(H4). The genomic G+C content was 70.2 mol%. Strain 10J was isolated from a biofilm of sediment microbial fuel cell, in Uruguay and had 99 % 16S rRNA gene sequence similarity to strain LZ-22T. DNA-DNA-hybridization values of 84 % confirmed that both strains belonged to the same species. Both strains grew on sugars, proteinaceous compounds, and some amino- and organic acids. Strain LZ-22T uniquely grew on D-enantiomers of histidine and valine while neglecting growth on L-enantiomers. Both strains were sensitive to most of the tested antibiotics but resistant to tested nitrofurans and sulfanilamides. Phylogenetic analyses of the 16S rRNA gene sequences indicated that the strains were related to members of the family Propionibacteriaceae (~93-94 % 16S rRNA gene sequence similarity) with formation of a separate branch within the radiation of the genera Granulicoccus and Luteococcus. Based on phenotypic and genotypic characteristics, we propose the affiliation of both strains into a novel species of a new genus. The name Raineyella antarctica gen. nov., sp. nov. is proposed for the novel taxon with the type strain LZ-22T (=ATCC TSD-18T=DSM 100494T=JCM 30886T).


Subject(s)
Bioelectric Energy Sources/microbiology , Lakes/microbiology , Phylogeny , Propionibacteriaceae/classification , Amino Acids/metabolism , Antarctic Regions , Bacteria, Anaerobic/classification , Bacteria, Anaerobic/genetics , Bacteria, Anaerobic/isolation & purification , Bacterial Typing Techniques , Base Composition , Biofilms , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Propionibacteriaceae/genetics , Propionibacteriaceae/isolation & purification , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Uruguay , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
14.
Antonie Van Leeuwenhoek ; 108(1): 151-61, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25980832

ABSTRACT

A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular methods was performed on three strains of a Gram-stain positive, non-sporeforming, motile aerobic rod-shaped bacterium resistant to tylosin and tetracycline isolated from a swine-manure storage pit. On the basis of 16S rRNA gene sequence analyses, it was confirmed that these isolates are highly related to each other and form a hitherto unknown lineage within the Planococcaceae. In particular, pairwise analysis of the 16S rRNA gene sequence demonstrated that the novel organism is closely related to members of the genus Sporosarcina (92.8-94.5 %), Pyschrobacillus (93.5-93.9 %) and Paenisporosarcina (93.3-94.5 %). The predominant fatty acids were found to consist of iso-C15:0 and iso-C17:1 ω10c and the G+C mol% was determined to be 41.8. Based on biochemical, chemotaxonomic, and phylogenetic evidence, it is proposed that these novel strains be classified as a novel genus and species, Savagea faecisuis gen nov., sp. nov. The type strain is Con12(T) (=CCUG 63563(T) = NRRL B-59945(T) = NBRC 109956(T)).


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial , Environmental Microbiology , Planococcaceae/classification , Planococcaceae/isolation & purification , Tetracycline/pharmacology , Tylosin/pharmacology , Aerobiosis , Animals , Base Composition , Cluster Analysis , Cytosol/chemistry , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Locomotion , Manure , Molecular Sequence Data , Phylogeny , Planococcaceae/drug effects , Planococcaceae/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Swine
15.
Anaerobe ; 32: 43-48, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25481562

ABSTRACT

A novel Gram-stain positive, non-motile, non-sporeforming coccus-shaped, obligately anaerobic bacterium was isolated from a fecal sample of an individual residing in a traditional Peruvian community. The organism was characterized using biochemical, chemotaxonomic and phylogenetic methods. Comparative 16S rRNA gene sequence analyses and phenotypic characteristics demonstrated that the organism was biochemically and phenotypically related, but distinct, from a group of organisms referred to as the Gram-stain positive anaerobic cocci (GPAC). The major cellular fatty acids of the novel isolate were determined to be C16:0 (18.3%), C18:1ω9c (39.8%), C18:2ω6,9c/C18:0 ANTE (13.2%). Fermentation end products from PYG are acetate and formate. Cell-wall peptidoglycan was found to be A4α (L-Lys-L-Ala-L-Glu) and the G + C content was determined to be 38.4 mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic results, Ezakiella peruensis gen. nov., sp. nov., is now proposed. The type strain is M6.X2(T) (DSM 27367(T) = NBRC 109957 (T) = CCUG 64571(T)).


Subject(s)
Carrier State , Feces/microbiology , Firmicutes/isolation & purification , Population Surveillance , Bacterial Typing Techniques , DNA, Bacterial , Firmicutes/chemistry , Firmicutes/classification , Firmicutes/genetics , Humans , Molecular Sequence Data , Peru , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics
17.
mSystems ; 2(3)2017.
Article in English | MEDLINE | ID: mdl-28680972

ABSTRACT

In an ongoing Microbial Observatory investigation of the International Space Station (ISS), 11 Bacillus strains (2 from the Kibo Japanese experimental module, 4 from the U.S. segment, and 5 from the Russian module) were isolated and their whole genomes were sequenced. A comparative analysis of the 16S rRNA gene sequences of these isolates showed the highest similarity (>99%) to the Bacillus anthracis-B. cereus-B. thuringiensis group. The fatty acid composition, polar lipid profile, peptidoglycan type, and matrix-assisted laser desorption ionization-time of flight profiles were consistent with the B. cereus sensu lato group. The phenotypic traits such as motile rods, enterotoxin production, lack of capsule, and resistance to gamma phage/penicillin observed in ISS isolates were not characteristics of B. anthracis. Whole-genome sequence characterizations showed that ISS strains had the plcR non-B. anthracis ancestral "C" allele and lacked anthrax toxin-encoding plasmids pXO1 and pXO2, excluding their identification as B. anthracis. The genetic identities of all 11 ISS isolates characterized via gyrB analyses arbitrarily identified them as members of the B. cereus group, but traditional DNA-DNA hybridization (DDH) showed that the ISS isolates are similar to B. anthracis (88% to 90%) but distant from the B. cereus (42%) and B. thuringiensis (48%) type strains. The DDH results were supported by average nucleotide identity (>98.5%) and digital DDH (>86%) analyses. However, the collective phenotypic traits and genomic evidence were the reasons to exclude the ISS isolates from B. anthracis. Nevertheless, multilocus sequence typing and whole-genome single nucleotide polymorphism analyses placed these isolates in a clade that is distinct from previously described members of the B. cereus sensu lato group but closely related to B. anthracis. IMPORTANCE The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station's surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions.

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