Characterization and survey in cattle of a rumen Pyrimadobacter sp. which degrades the plant toxin fluoroacetate

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Seungha Kang ◽  
Shahjalal Khan ◽  
Rick Webb ◽  
Stuart Denman ◽  
Chris McSweeney
Keyword(s):  
Amino Acids ◽  
Cell Envelope ◽  
Rumen Bacterium ◽  
Rrna Gene ◽  
Plant Toxin ◽  
Cavity Transmission ◽  
Transmission Electron ◽  
Gene Sequence Analysis ◽  
Degrading Bacteria ◽  
Bacterium Strain

ABSTRACT Among the natural halogenic compounds, the plant toxin fluoroacetate (FA) causes livestock fatalities in southern hemisphere countries. Here, we report on the isolation of a rumen bacterium, strain C12–8 that degrades FA under anaerobic conditions. 16S rRNA gene sequence analysis showed this bacterium belonged to the Pyramidobacter genus within the Synergistetes phylum and was 98% similar to Pyramidobacter piscolens W5455 isolated from the human oral cavity. Transmission electron microscopy showed the cell envelope to be unusual, with only one membrane and no obvious external wall. Growth and FA degradation were enhanced by peptide-rich protein hydrolysates but not carbohydrates. End products of metabolism were mainly acetate, propionate/isovalerate and isobutyrate. Strain C12-8 preferentially used peptide-bound amino acids rather than free amino acids. Glycine, serine, threonine, leucine, histidine and isoleucine were utilized as free and peptide-bound amino acids, but there was minimal utilization of alanine, proline, methionine, aspartic acid, lysine and arginine in either form. A survey of several cattle properties in northern Australia showed that strain C12-8 and other FA degrading bacteria affiliated with Cloacibacillus porcorum strain MFA1 were endemic to cattle in the northern beef herd and may help to reduce toxicity.

scholarly journals Fervidobacterium changbaicum sp. nov., a novel thermophilic anaerobic bacterium isolated from a hot spring of the Changbai Mountains, China

2007 ◽  
Vol 57 (10) ◽  
pp. 2333-2336 ◽  
Author(s):  
Jingang Cai ◽  
Yanping Wang ◽  
Dongbo Liu ◽  
Yan Zeng ◽  
Yanfen Xue ◽  
...  
Keyword(s):  
Hot Spring ◽  
Cell Envelope ◽  
Carbon Sources ◽  
Optimal Growth ◽  
Changbai Mountains ◽  
Rrna Gene ◽  
High Concentration ◽  
Gene Sequence Analysis ◽  
Wide Range ◽  
Bacterium Strain

A thermophilic, obligately anaerobic, rod-shaped bacterium (strain CBS-1T) was isolated from a hot spring mixture of water and mud of the Changbai Mountains, China. Strain CBS-1T was found to be non-sporulating, Gram-negative, with optimal growth at 75–80 °C. It grew on a wide range of carbon sources, including glucose, lactose, maltose, starch, sorbitol and pyruvate amongst others. The DNA G+C content of strain CBS-1T was 31.9 mol%. The 16S rRNA gene sequence analysis indicated that the strain was a member of the genus Fervidobacterium. The high concentration of C16 : 0 (52.2 %) in the fatty acid profile of the cell envelope supported its inclusion as a member of the genus Fervidobacterium. On the basis of the low values of DNA–DNA hybridization (25.8 and 20.5 %) and phenotypic features, strain CBS-1T represents a novel species of the genus Fervidobacterium, for which the name Fervidobacterium changbaicum sp. nov. is proposed. The type strain is CBS-1T (=DSM 17883T=JCM 13353T).

scholarly journals Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2831-2837 ◽  
Author(s):  
Peter Kämpfer ◽  
Karin Martin ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

scholarly journals Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis

2018 ◽  
Vol 6 (14) ◽  
Author(s):  
Sarah Hahnke ◽  
Christian Abendroth ◽  
Thomas Langer ◽  
Francisco M. Codoñer ◽  
Patrice Ramm ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biomass Hydrolysis ◽  
Content Type ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Bacterium Strain ◽  
Anaerobic Biomass

ABSTRACT A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcaceae outside recently described genera.

Blastochloris gulmargensis sp. nov., isolated from an epilithic phototrophic biofilm

2011 ◽  
Vol 61 (8) ◽  
pp. 1811-1816 ◽  
Author(s):  
V. Venkata Ramana ◽  
Shivali Kapoor ◽  
E. Shobha ◽  
E. V. V. Ramprasad ◽  
Ch. Sasikala ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phototrophic Biofilm ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Blastochloris Viridis

A novel Gram-negative, motile, bacteriochlorophyll b-containing purple non-sulfur bacterium, strain JA248T, was isolated from phototrophic enrichments of a yellow–green epilithic biofilm sample collected from Gulmarg, India. The genomic DNA G+C content of strain JA248T was 63.8 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA248T had highest similarity to members of the genus Blastochloris and was closely related to Blastochloris sulfoviridis DSM 729T (98.5 % sequence similarity) and Blastochloris viridis DSM 133T (98.4 %) of the class Alphaproteobacteria. Strain JA248T was characterized based on polyphasic taxonomy, and distinct phenotypic and molecular differences based on DNA–DNA hybridization (relatedness of <46.5 % with the two species of the genus Blastochloris), multilocus sequence analysis, and phenotypic and chemotaxonomic evidence separated strain JA248T from other species of the genus Blastochloris. Strain JA248T therefore represents a novel species in the genus Blastochloris, for which the name Blastochloris gulmargensis sp. nov. is proposed. The type strain is JA248T ( = JCM 14795T  = DSM 19786T).

scholarly journals Slackia equolifaciens sp. nov., a human intestinal bacterium capable of producing equol

2010 ◽  
Vol 60 (8) ◽  
pp. 1721-1724 ◽  
Author(s):  
Jong-Sik Jin ◽  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Masao Hattori ◽  
Yoshimi Benno
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Dimethyl Acetal ◽  
Rrna Gene ◽  
Intestinal Bacterium ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

An equol-producing bacterium, strain DZET, which was isolated from human faeces, was characterized by morphological, biochemical and molecular methods. The isolate was Gram-positive, obligately anaerobic, non-spore-forming, asaccharolytic and rod-shaped. 16S rRNA gene sequence analysis showed 92.8, 91.0, 91.1 and 90.6 % similarities with Slackia faecicanis, Slackia exigua, Slackia heliotrinireducens and Slackia isoflavoniconvertens, respectively. Based on these data, we propose a novel species of the genus Slackia, Slackia equolifaciens sp. nov. The major cellular fatty acids are C14 : 0, C18 : 1 ω9c and C18 : 1 ω9c DMA (dimethyl acetal). The DNA G+C content of the strain is 60.8 mol%. The type strain of S. equolifaciens sp. nov. is DZET (=JCM 16059T =CCUG 58231T).

Microbulbifer chitinilyticus sp. nov. and Microbulbifer okinawensis sp. nov., chitin-degrading bacteria isolated from mangrove forests

2011 ◽  
Vol 61 (9) ◽  
pp. 2215-2220 ◽  
Author(s):  
Atsushi Baba ◽  
Masayuki Miyazaki ◽  
Takahiko Nagahama ◽  
Yuichi Nogi
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Threshold Level ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Mangrove Forests ◽  
The Novel ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
Degrading Bacteria

Three chitin-degrading strains representing two novel species were isolated from mangrove forests in Okinawa, Japan. The isolates, ABABA23T, ABABA211 and ABABA212T, were Gram-negative, non-spore-forming, strictly aerobic chemo-organotrophs. The novel strains produced Q-8 as the major isoprenoid quinone component. The predominant fatty acids were iso-C15 : 0 and C16 : 0. On the basis of 16S rRNA gene sequence analysis, the isolates were closely affiliated with members of the genus Microbulbifer. The DNA G+C contents of strains ABABA23T and ABABA212T were 57.8 and 60.2 mol%, respectively. DNA–DNA relatedness values between these two strains and Microbulbifer reference strains were significantly lower than 70 %, the generally accepted threshold level below which strains are considered to belong to separate species. Based on differences in taxonomic characteristics, the three isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer chitinilyticus sp. nov. (type strain, ABABA212T = JCM 16148T = NCIMB 14577T) and Microbulbifer okinawensis sp. nov. (type strain, ABABA23T = JCM 16147T = NCIMB 14576T; reference strain, ABABA211) are proposed.

scholarly journals Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment

2011 ◽  
Vol 61 (2) ◽  
pp. 281-285 ◽  
Author(s):  
Mi-Hak Park ◽  
Jitsopin Traiwan ◽  
Min Young Jung ◽  
Yun Sung Nam ◽  
Ji Hoon Jeong ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Tidal Flat Sediment ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).

scholarly journals Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 591-595 ◽  
Author(s):  
Sang-Hee Lee ◽  
Qing-Mei Liu ◽  
Sung-Taik Lee ◽  
Sun-Chang Kim ◽  
Wan-Taek Im
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Bacterium Strain

A Gram-reaction-positive, rod-shaped, non-motile, non-spore-forming bacterium (strain BX5-10T) was isolated from the soil of a ginseng field on Baekdu Mountain in Jilin district, China. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain BX5-10T was shown to belong to the family Nocardioidaceae and to be most closely related to Nocardioides plantarum NCIMB 12834T (96.5 % sequence similarity), Nocardioides dokdonensis KCTC 19309T (96.2 %) and Nocardioides fonticola NAA-13T (95.1 %). Strain BX5-10T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C18 : 1ω9c, C16 : 0 and C17 : 1ω8c as its major fatty acids. The G+C content of the genomic DNA was 70.3 mol%. The novel strain could be differentiated genotypically and phenotypically from all recognized species of the genus Nocardioides. Based on the results of the phylogenetic analyses and the genotypic and phenotypic data, a novel species, Nocardioides ginsengagri sp. nov., is proposed. The type strain is BX5-10T ( = KCTC 19467T = DSM 21362T).

scholarly journals Anaerobic Degradation of 4-Methylbenzoate by a Newly Isolated Denitrifying Bacterium, Strain pMbN1

2011 ◽  
Vol 78 (5) ◽  
pp. 1606-1610 ◽  
Author(s):  
Sven Lahme ◽  
Jens Harder ◽  
Ralf Rabus
Keyword(s):  
Aromatic Compounds ◽  
Anaerobic Degradation ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Denitrifying Bacterium ◽  
Reducing Conditions ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

ABSTRACTA novel alphaproteobacterium isolated from freshwater sediments, strain pMbN1, degrades 4-methylbenzoate to CO2under nitrate-reducing conditions. While strain pMbN1 utilizes several benzoate derivatives and other polar aromatic compounds, it cannot degradep-xylene or other hydrocarbons. Based on 16S rRNA gene sequence analysis, strain pMbN1 is affiliated with the genusMagnetospirillum.

scholarly journals Brachybacterium zhongshanense sp. nov., a cellulose-decomposing bacterium from sediment along the Qijiang River, Zhongshan City, China

2007 ◽  
Vol 57 (11) ◽  
pp. 2519-2524 ◽  
Author(s):  
Guoxia Zhang ◽  
Guoqu Zeng ◽  
Xiaowei Cai ◽  
Suier Deng ◽  
Huidong Luo ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Insertion Sequence ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Ratio Analysis ◽  
Polyphasic Analysis ◽  
Hybridization Data ◽  
Dna Base ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A cellulose-decomposing bacterium, strain JBT, was isolated from sediments along the Qijiang River, Zhongshan City, China. Results of morphological, biochemical and chemotaxonomic characterization and 16S rRNA gene sequence analysis revealed that strain JBT belonged to the genus Brachybacterium. Insertion sequence-PCR fingerprinting patterns, DNA base ratio analysis and DNA–DNA hybridization data showed that strain JBT differed from recognized species of the genus Brachybacterium. Based on polyphasic analysis, strain JBT represents a novel species of the genus Brachybacterium, for which the name Brachybacterium zhongshanense sp. nov. is proposed. The type strain is JBT (=LMG 23926T=CGMCC 1.6508T=DSM 18832T).

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