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Kim HS, Kim JS, Suh MK, Eom MK, Lee J, Lee JS. A novel plant growth-promoting rhizobacterium, Rhizosphaericola mali gen. nov., sp. nov., isolated from healthy apple tree soil. Sci Rep 2024; 14:1038. [PMID: 38200134 PMCID: PMC10781739 DOI: 10.1038/s41598-024-51492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024] Open
Abstract
The rhizosphere microbial community is closely associated with plant disease by regulating plant growth, agricultural production, nutrient availability, plant hormone and adaptation to environmental changes. Therefore, it is very important to identify the rhizosphere microbes around plant roots and understand their functions. While studying the differences between the rhizosphere microbiota of healthy and diseased apple trees to find the cause of apple tree disease, we isolated a novel strain, designated as B3-10T, from the rhizosphere soil of a healthy apple tree. The genome relatedness indices between strain B3-10T and other type species of family Chitinophagaceae were in the ranges of 62.4-67.0% for ANI, 18.6-32.1% for dDDH, and 39.0-56.6% for AAI, which were significantly below the cut‑off values for the species delineation, indicating that strain B3-10T could be considered to represent a novel genus in family Chitinophagaceae. Interestingly, the complete genome of strain B3-10T contained a number of genes encoding ACC-deaminase, siderophore production, and acetoin production contributing to plant-beneficial functions. Furthermore, strain B3-10T was found to significantly promote the growth of shoots and roots of the Nicotiana benthamiana, which is widely used as a good model for plant biology, demonstrating that strain B3-10T, a rhizosphere microbe of healthy apple trees, has the potential to promote growth and reduce disease. The phenotypic, chemotaxonomic, phylogenetic, genomic, and physiological properties of this plant growth-promoting (rhizo)bacterium, strain B3-10T supported the proposal of a novel genus in the family Chitinophagaceae, for which the name Rhizosphaericola mali gen. nov., sp. nov. (= KCTC 72123T = NBRC 114178T).
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Affiliation(s)
- Han Sol Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea.
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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Han J, Aljahdali N, Zhao S, Tang H, Harbottle H, Hoffmann M, Frye JG, Foley SL. Infection biology of Salmonella enterica. EcoSal Plus 2024:eesp00012023. [PMID: 38415623 DOI: 10.1128/ecosalplus.esp-0001-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/31/2023] [Indexed: 02/29/2024]
Abstract
Salmonella enterica is the leading cause of bacterial foodborne illness in the USA, with an estimated 95% of salmonellosis cases due to the consumption of contaminated food products. Salmonella can cause several different disease syndromes, with the most common being gastroenteritis, followed by bacteremia and typhoid fever. Among the over 2,600 currently identified serotypes/serovars, some are mostly host-restricted and host-adapted, while the majority of serotypes can infect a broader range of host species and are associated with causing both livestock and human disease. Salmonella serotypes and strains within serovars can vary considerably in the severity of disease that may result from infection, with some serovars that are more highly associated with invasive disease in humans, while others predominantly cause mild gastroenteritis. These observed clinical differences may be caused by the genetic make-up and diversity of the serovars. Salmonella virulence systems are very complex containing several virulence-associated genes with different functions that contribute to its pathogenicity. The different clinical syndromes are associated with unique groups of virulence genes, and strains often differ in the array of virulence traits they display. On the chromosome, virulence genes are often clustered in regions known as Salmonella pathogenicity islands (SPIs), which are scattered throughout different Salmonella genomes and encode factors essential for adhesion, invasion, survival, and replication within the host. Plasmids can also carry various genes that contribute to Salmonella pathogenicity. For example, strains from several serovars associated with significant human disease, including Choleraesuis, Dublin, Enteritidis, Newport, and Typhimurium, can carry virulence plasmids with genes contributing to attachment, immune system evasion, and other roles. The goal of this comprehensive review is to provide key information on the Salmonella virulence, including the contributions of genes encoded in SPIs and plasmids during Salmonella pathogenesis.
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Affiliation(s)
- Jing Han
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Nesreen Aljahdali
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
- Biological Science Department, College of Science, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Hailin Tang
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Heather Harbottle
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jonathan G Frye
- Agricutlutral Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | - Steven L Foley
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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Li FX, Zhao WH, Li ZH, Song JL, Gao HF. Moraxella haemolytica sp. nov., isolated from a goat with respiratory disease. Arch Microbiol 2023; 206:45. [PMID: 38153526 DOI: 10.1007/s00203-023-03782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/29/2023]
Abstract
An aerobic, haemolytic, Gram-negative and rod-shaped bacterial strain ZY171148T was isolated from the lung of a dead goat with respiratory disease in Southwest China. The strain grew at 24-39 °C, at pH 6.0-9.0 and in the presence of 0.5-2.0% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belongs to the genus Moraxella. The nucleotide sequence similarity analysis of the 16S rRNA gene showed that the strain has the highest similarity of 98.1% to Moraxella (M.) caprae ATCC 700019 T. Phylogenomic analysis of 800 single-copy protein sequences indicated that the strain is a member of the genus Moraxella and forms a separated branch on the Moraxella phylogenetic tree. The strain exhibited the highest orthologous average nucleotide identity (OrthoANI) and average amino acid identity (AAI) values of 77.0 and 77.9% to M. nasibovis CCUG 75921T and M. ovis CCUG 354T, respectively. The strain shared the highest digital DNA-DNA hybridization (dDDH) value of 26.2% to M. osloensis CCUG 350T. The genome G + C content of strain ZY171148T was 42.6 mol%. The strain had C18:1 ω9c (41.7%), C18:0 (11.2%), C16:0 (14.1%) and C12:0 3OH (9.7%) as the predominant fatty acids and CoQ-8 as the major respiratory quinone. The strain contained phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, dilysocardiolipin, monolysocardiolipin and phosphatidic acid as the major polar lipids. β-haemolysis was observed on Columbia blood agar. All results confirmed that strain ZY171148T represents a novel species of the genus Moraxella, for which the name Moraxella haemolytica sp. nov. is proposed, with strain ZY171148T = CCTCC AB 2021471T = CCUG 75920T as the type strain.
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Affiliation(s)
- Fu-Xiang Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China.
| | - Wen-Hua Zhao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Zhan-Hong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Jian-Ling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Hua-Feng Gao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
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Habenicht T, Weidenbach K, Velazquez-Campoy A, Buey RM, Balsera M, Schmitz RA. Small protein mediates inhibition of ammonium transport in Methanosarcina mazei-an ancient mechanism? Microbiol Spectr 2023; 11:e0281123. [PMID: 37909787 PMCID: PMC10714827 DOI: 10.1128/spectrum.02811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Small proteins containing fewer than 70 amino acids, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role of the small protein sP36 in the nitrogen metabolism of M. mazei, which modulates the ammonium transporter AmtB1 according to nitrogen availability. This modulation might represent an ancient archaeal mechanism of AmtB1 inhibition, in contrast to the well-studied uridylylation-dependent regulation in bacteria.
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Affiliation(s)
- Tim Habenicht
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katrin Weidenbach
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigaciones Sanitarias de Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ruben M. Buey
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Monica Balsera
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Spanish National Research Council (IRNASA-CSIC), Salamanca, Spain
| | - Ruth A. Schmitz
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Kim HS, Suh MK, Kim JS, Do HE, Eom MK, Jin JS, Lee JS. Pseudomonas aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 38047902 DOI: 10.1099/ijsem.0.006190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Two novel Pseudomonas strains, SA3-5T and SA3-6, were isolated from a tidal flat (getbol) in the Republic of Korea. Strains SA3-5T and SA3-6 were subjected to polyphasic characterization to determine their taxonomic affiliations. Cells were Gram-stain-negative, aerobic, rod-shaped and motile by using peritrichous flagella. Based on their 16S rRNA gene sequences, strains SA3-5T and SA3-6 exhibited a high degree of similarity (100 %) and were classified within the genus Pseudomonas. Furthermore, the closest related species to SA3-5T and SA3-6 were Pseudomonas taeanensis MS-3T (98.3 %). The ranges of average nucleotide identity and digital DNA-DNA hybridization values between SA3-5T and closely related species were 75.9-89.1% and 21.3-38.7%, respectively, both of which being below the thresholds for delineating novel strains. Strain SA3-5T and SA3-6 contained C16 : 1 ω6с and/or C16 : 1 ω7с (summed feature 3), C16 : 0 and C18 : 1 ω6с and/or C18 : 1 ω7с (summed feature 8) as the major fatty acids. The predominant respiratory quinone was Q-9. The DNA G+C content of strain SA3-5T was 62.5 mol%. Based on their combined phenotypic, chemotaxonomic and phylogenetic characterisitics, strains SA3-5T and SA3-6 represent a novel species of the genus Pseudomonas for which the name Pseudomonas aestuarii sp. nov. is proposed. The type strain is SA3-5T (=KCTC 92395T=JCM 35697T).
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Affiliation(s)
- Han Sol Kim
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
| | - Hyo Eun Do
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si54596,Jeollabuk-do, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si54596,Jeollabuk-do, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- University of Science and Technology(UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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Zhou ZY, An J, Jia YW, Xuan XQ, Du ZJ. Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37942742 DOI: 10.1099/ijsem.0.006155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
Two novel rod-shaped, Gram-stain-negative, aerobic and non-motile bacterial strains, designated M39T and C2-7T, were isolated from the coastal sediment of Xiaoshi Island, Weihai, PR China. Growth of strain M39T occurred at 15-37 °C, at pH 6.0-9.0 and in the presence of 1.0-9.0 % (w/v) NaCl. Strain C2-7T grew at 15-40 °C, at pH 6.0-8.0 and in the presence of 0.5-8.0 % (w/v) NaCl. Phylogenetic analysis based 16S rRNA gene sequences revealed that strains M39T and C2-7T belong to the phylum Bacteroidota. Based on the results of 16S rRNA gene sequence analysis, the closest relative of strain M39T was Robiginitalea marina KCTC 92035T (95.4 %), and the closest relative of strain C2-7T was Algoriphagus namhaensis DPG-3T (97.0 %). The percentage of conserved protein and average nucleotide identity values between strain M39T and some species of the genus Robiginitalea were 66.9-77.6% and 69.3-71.0 %, respectively, while those between strain C2-7T and some species of the genus Algoriphagus were 68.0-70.1% and 56.1-72.6 %, respectively. The major cellular fatty acids (>10 %) of strain M39T consisted of iso-C15 : 1 F, iso-C15 : 0 and iso-C17 : 0 3-OH, while those of strain C2-7T were iso-C15 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. MK-6 was the only respiratory quinone that was compatible with the genus of strain M39T. The predominant menaquinone of strain C2-7T was MK-7. The major polar lipids of strain M39T were phosphatidylethanolamine and glycolipids, and those of strain C2-7T were phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. The DNA G+C contents of strains M39T and C2-7T were 46.9 and 40.8 mol%, respectively. Based upon the results presented in this study, strains M39T and C2-7T represent novel species of the genera Robiginitalea and Algoriphagus, respectively, for which the names Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov. are proposed with the type strains M39T (=MCCC 1H00498T=KCTC 92014T) and C2-7T (=MCCC 1H00414T=KCTC 92027T).
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Affiliation(s)
- Zi-Yang Zhou
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Jing An
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Ya-Wei Jia
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Xiao-Qi Xuan
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, PR China
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Wang SX, Wang YW, Ma L, An J, Gong Y, Du ZJ. Winogradskyella immobilis sp. nov., an Alginate-Hydrolyzing Bacterium Isolated from the Brown Algae Saccharina japonica. Curr Microbiol 2023; 80:370. [PMID: 37838638 DOI: 10.1007/s00284-023-03474-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/04/2023] [Indexed: 10/16/2023]
Abstract
A novel bacterium, designated E313T, was isolated from brown algae Saccharina japonica in Weihai, China. The strain is a Gram-stain-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium that grows optimally at 28 °C with pH levels between 7.0 and 7.5 and in the presence of 2-3% (w/v) NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence placed the strain within the monophyletic cluster of the genus Winogradskyella, exhibiting the highest similarity to Winogradskyella wandonensis KCTC 32579T (96.8%). Genome comparison of strain E313T with W. wandonensis KCTC 32579T and W. thalassocola KCTC 12221T revealed average nucleotide identity (ANI) values of 74.2% and 74.8%, and DNA-DNA hybridization (dDDH) values of 19.0% and 19.5%, respectively, lower than prokaryotic species delineation values. The strain E313T could hydrolyze alginate. A total of 123 carbohydrate-active enzymes were annotated according to the CAZy database. Especially, one oligo-alginate lyase and one poly(β-D-mannuronate) lyase were identified in the genome of strain E313T. Strain E313T possessed MK-6 quinone and iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and iso-C15:0 3-OH as main fatty acids. Its major polar lipids were phosphatidylethanolamine (PE), one unidentified aminolipid, and two unknown lipids. Thus, based on phylogenetic, physiological, and chemotaxonomic analyses, we propose a novel species of the genus Winogradskyella, named Winogradskyella immobilis sp. nov., with E313T (= MCCC 1H00506T = KCTC 82731T) as the type strain.
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Affiliation(s)
- Shu-Xin Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Lu Ma
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing An
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Ya Gong
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, China.
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, China.
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Pavlova ON, Tupikin AE, Chernitsyna SM, Bukin YS, Lomakina AV, Pogodaeva TV, Nikonova AA, Bukin SV, Zemskaya TI, Kabilov MR. Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal. MICROBIAL ECOLOGY 2023; 86:1604-1619. [PMID: 36717392 DOI: 10.1007/s00248-023-02182-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151T), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.
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Affiliation(s)
- O N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
| | - A E Tupikin
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - S M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Y S Bukin
- Laboratory of Genosystematics, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A V Lomakina
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A A Nikonova
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - S V Bukin
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - M R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Li Z, Zhou X, Liao D, Liu R, Zhao X, Wang J, Zhong Q, Zeng Z, Peng Y, Tan Y, Yang Z. Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials. Front Cell Infect Microbiol 2023; 13:1180194. [PMID: 37662009 PMCID: PMC10471985 DOI: 10.3389/fcimb.2023.1180194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations. Methods This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted. Results General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies. Disucssion This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.
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Affiliation(s)
- Zijiao Li
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xiang Zhou
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Danxi Liao
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Ruolan Liu
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xia Zhao
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Jing Wang
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zhuo Zeng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yizhi Peng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yinling Tan
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zichen Yang
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
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Chen RY, Chen RJ, Lu DC, Gong Y, Du ZJ. Pontibacterium sinense sp. nov., a nitrate-reducing and thiosulphate-oxidizing bacterium, isolated from coastal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37610813 DOI: 10.1099/ijsem.0.006018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
A novel bacterial strain, N1Y112T, was isolated from coastal sediment collected in Weihai, PR China. This Gram-stain-negative, facultatively anaerobic, motile rod-shaped bacterium exhibited the ability to oxidize thiosulphate to sulphate and reduce nitrate to ammonia through its Sox system and nitrate reduction pathway, respectively. The strain grew at 20-35 °C (optimum, 28 °C), pH 6.0-10.0 (optimum, pH 7.5) and in the presence of 1.0-5.0 % (w/v) NaCl (optimum, 3.0 %). Major fatty acids present in the strain included summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. Its polar lipid profile consisted of one phosphatidylethanolamine, two unknown aminolipids, one aminophosphoglycolipid, one diphosphatidylglycerol, one phosphatidylglycerol, two unknown phospholipids and two unknown lipids. Strain N1Y112T contained ubiquinone-7 and ubiquinone-8 as isoprenoid quinones, with a genomic G+C content of 50.6 mol%. Based on phylogenetic analysis, strain N1Y112T clustered with Pontibacterium granulatum JCM 30316T being its closest relative at 97.1 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA-DNA hybridization values were 77.1 and 20.7 %, respectively, which suggest significant differences between genomes of N1Y112T and P. granulatum JCM 30316T. Based on the findings from its phenotypic, genotypic and phylogenetic analyses, N1Y112T is considered to represent a novel species of the genus Pontibacterium, for which the name Pontibacterium sinense sp. nov. is proposed. The type strain is N1Y112T (=KCTC 72927T=MCCC 1H00429T).
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Affiliation(s)
- Rui-Ying Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Rui-Jie Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - De-Chen Lu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya Gong
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, Shandong, 264209, PR China
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11
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Li F, Zhao W, Zhu P, Li Z, Song J, Zhu J, Gao H. Moraxella nasibovis sp. nov., Isolated from a Cow with Respiratory Disease. Curr Microbiol 2023; 80:305. [PMID: 37493823 DOI: 10.1007/s00284-023-03415-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Strain ZY190618T, isolated from the nasal cavity of a cow with respiratory disease, was subjected to taxonomic characterization. Cells of the strain were Gram-stain-negative, aerobic and coccus-shaped. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that the strain belonged to the genus Moraxella with the highest similarity of 98.1% to Moraxella nasovis CCUG 75922T. Phylogenomic analysis based on 810 single-copy genes revealed that the strain was a member of the genus Moraxella and formed a deep and separated clade within the genus. The strain showed the highest orthologous average nucleotide identity (OrthoANI) value of 77.1% with Moraxella ovis CCUG 354T and digital DNA-DNA hybridization (dDDH) value of 24.7% with Moraxella equi NCTC 11012T, respectively. The DNA G + C content was 46.5 mol%. The strain optimally grew at 37 °C (temperature range, 24-42 °C), at pH 8.0 (pH range, 6.0-9.0) and with 1.5% (w/v) NaCl (NaCl range, 0.5-3.0%). The strain contained C18:1 ω9c as the sole predominant fatty acid (> 5 %) and CoQ-8 as the major respiratory quinone. The major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, monolysocardiolipin and hemibismonoacylglycerophosphate. Based on these data, strain ZY190618T clearly represents a novel species in the genus Moraxella, for which the name Moraxella nasibovis sp. nov. (The type strain ZY190618T = CCUG 75921T = CCTCC AB 2021472T) is proposed.
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Affiliation(s)
- Fuxiang Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Wenhua Zhao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Pei Zhu
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Jianling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Jianbo Zhu
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Huafeng Gao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China.
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Soares-Castro P, Soares F, Reis F, Lino-Neto T, Santos PM. Bioprospection of the bacterial β-myrcene-biotransforming trait in the rhizosphere. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12650-w. [PMID: 37405434 PMCID: PMC10386936 DOI: 10.1007/s00253-023-12650-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023]
Abstract
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr+). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr+ isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr+-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr+ bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr+ trait is spread across different bacterial taxonomic classes. • The core-code for the Myr+ trait was detected in a novel ICE, only found in Pseudomonas spp.
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Affiliation(s)
- Pedro Soares-Castro
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal
| | - Filipa Soares
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Francisca Reis
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Teresa Lino-Neto
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro M Santos
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal.
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Bertrand CDF, Martins R, Quintas-Nunes F, Reynolds-Brandão P, Crespo MTB, Nascimento FX. Saccharopolyspora sp. NFXS83 in Marine Biotechnological Applications: From Microalgae Growth Promotion to the Production of Secondary Metabolites. Microorganisms 2023; 11:microorganisms11040902. [PMID: 37110324 PMCID: PMC10145562 DOI: 10.3390/microorganisms11040902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Marine bacteria are a significant source of bioactive compounds for various biotechnological applications. Among these, actinomycetes have been found to produce a wide range of secondary metabolites of interest. Saccharopolyspora is one of the genera of actinomycetes that has been recognized as a potential source of these compounds. This study reports the characterization and genomic analysis of Saccharopolyspora sp. NFXS83, a marine bacterium isolated from seawater from the Sado estuary in Portugal. The NFXS83 strain produced multiple functional and stable extracellular enzymes under high-salt conditions, showed the ability to synthesize auxins such as indole-3-acetic acid, and produced diffusible secondary metabolites capable of inhibiting the growth of Staphylococcus aureus. Furthermore, when Phaeodactylum tricornutum was co-cultivated with strain NFXS83 a significant increase in microalgae cell count, cell size, auto-fluorescence, and fucoxanthin content was observed. Detailed analysis revealed the presence of clusters involved in the production of various secondary metabolites, including extracellular enzymes, antimicrobial compounds, terpenes, and carotenoids in the genome of strain NFXS83. Ultimately, these findings indicate that Saccharopolyspora sp. NFXS83 has a significant potential for a wide range of marine biotechnological applications.
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Petrigna L, Petta A, Giustino V, Leale I, Pillitteri G, Palma A, Zangla D, Battaglia G. A scoping review on how physical fitness is evaluated in sitting volleyball players. J Sports Med Phys Fitness 2023; 63:430-435. [PMID: 35816141 DOI: 10.23736/s0022-4707.22.13982-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
INTRODUCTION Sitting volleyball is a widely practiced paralympic sport. A correct and standardized physical evaluation helps coaches to plan and manage the training. It is also important to evaluate physical fitness accurately and adopt standardized protocols to compare and normalize the data. The aim of the study was to evaluate physical fitness evaluation methods adopted in sitting volleyball and to eventually propose standard operating procedures. EVIDENCE ACQUISITION English-written and peer-reviewed original articles were included in this review. The population studied was composed only of athletes practicing sitting volleyball. Articles were searched on the electronic databases PubMed, Web of Science, and Scopus using keywords matched with Boolean operators. Two independent investigators collected and screened the studies against the eligibility criteria. Data were analyzed narratively. EVIDENCE SYNTHESIS Only 7 studies were eligible and included in this review, but a wide testing methodology exists. There are some tests commonly adopted in the studies included and these are the handgrip test, the agility t-test, the speed, and endurance test. These tests with the 2-site skinfold thickness evaluation, the modified push-ups, the shoulder-stretch test, the chest throw test and the simple reaction time task were included in the standard operating procedure. CONCLUSIONS The literature on the topic is poor and standardization of the testing procedure to evaluate the physical fitness of people practicing SV has been provided.
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Affiliation(s)
- Luca Petrigna
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy - .,School of Medicine, Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Science, University of Catania, Catania, Italy -
| | - Antonina Petta
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
| | - Valerio Giustino
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
| | - Ignazio Leale
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
| | - Guglielmo Pillitteri
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
| | - Antonio Palma
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
| | - Daniele Zangla
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
| | - Giuseppe Battaglia
- Sports and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Palermo, Italy
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Draft Genome Sequences of 14 Fluoroquinolone-Resistant Escherichia coli Isolates from Imported Shrimp. Microbiol Resour Announc 2023; 12:e0111622. [PMID: 36856408 PMCID: PMC10112127 DOI: 10.1128/mra.01116-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
We report the draft genome sequences of 14 fluoroquinolone-resistant Escherichia coli strains that were isolated from imported shrimp. All isolates contained multiple point mutations in the quinolone resistance-determining regions (QRDRs) and non-QRDRs of gyrA, parC, and parE genes. The data improve the understanding of fluoroquinolone resistance and indicate resistance mechanisms.
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Nitratireductor luteus sp. nov. isolated from saline-alkali land. Antonie Van Leeuwenhoek 2023; 116:221-229. [PMID: 36462113 DOI: 10.1007/s10482-022-01797-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022]
Abstract
The Gram-staining negative, oxidase and catalase negative strain KC-ST17T, isolated from saline-alkali land, was characterized using a polyphasic approach to determine its taxonomic position. Using 16S rRNA gene sequence analysis, the highest similarity of strain KC-ST17T was found with Nitratireductor pacificus CCTCC AB 209302T (97.2%). Cells are aerobic, non-motile, and rod-shaped. The isolate was found to be able to grow in NaCl concentrations of 0-4.0%. The assembled genome of strain KC-ST17T had a total length of 4.9 Mb with a G + C content of 62.7%. According to genome analysis, strain KC-ST17T encodes genes involved in the reduction of nitrate to nitrite, which may play a role in the utilization of nitrogenous compounds from the soil as an immediate source of energy. Based on the phenotypic characteristics and phylogenetic analysis, strain KC-ST17T was confirmed to represent a novel species in the Nitratireductor genus; thus, the name Nitratireductor luteus sp. nov. was proposed. The type strain of this species was KC-ST17T (= KCTC 92119T = MCCC 1K07309T).
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Li F, Gao H, Zhu P, Li Z, Zhao W, Song J, Yang S. Moraxella nasicaprae sp. nov., Isolated from a Goat with Respiratory Disease. Curr Microbiol 2023; 80:78. [PMID: 36651991 DOI: 10.1007/s00284-023-03185-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
A novel Gram-stain-negative, aerobic, irregular coccus designated as ZY201224T, was isolated from the nasal cavity of a goat with respiratory disease in a goat farm, located at Jianshui, Yunnan Province, PR China and its taxonomic position was clarified using a polyphasic approach. The strain grew optimally at 37 °C, at pH 8.0 and in the presence of 1% NaCl. Phylogenetic analysis based on 16S rRNA gene sequence and phylogenomic analysis based on 808 single-copy genes revealed that the strain is affiliated to the genus Moraxella and is distinct from the recognized species of the genus. The 16S rRNA gene sequence similarity analysis indicated that the strain is most closely related to Moraxella caviae CCUG 355T with sequence similarity of 98.1%. The genomic OrthoANI and digital DNA-DNA hybridization (dDDH) values between the strain and the type strains of Moraxella species were no higher than 74.7% (Moraxella pluranimalium CCUG 54913T) and 26.0% (Moraxella oblonga NBRC 102422T), respectively. The G + C content of the complete genome sequence was 43.6 mol%. The strain contained CoQ-8 as the major respiratory quinone, and C18:1ω9c, C17:1ω8c, C16:0 and summed feature 3 (C16:1 ω7c and/ or C16:1ω6c) as the predominant fatty acids (> 5%). The major polar lipids comprised phosphatidylglycerol (PG), cardiolipin (CL), monolysocardiolipin (MLCL), phosphatidylethanolamine (PE) and lysophosphatidylglycerol (LPG). Based on these taxonomic characterizations, strain ZY201224T represents a novel species of the genus Moraxella, for which the name Moraxella nasicaprae sp. nov. is proposed. The type strain is ZY201224T (= CCTCC AB 2021474T = NBRC 115473T).
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Affiliation(s)
- Fuxiang Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Huafeng Gao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Pei Zhu
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Wenhua Zhao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Jianling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Shibiao Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China.
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Lutfullin MT, Lutfullina GF, Pudova DS, Akosah YA, Shagimardanova EI, Vologin SG, Sharipova MR, Mardanova AM. Identification, characterization, and genome sequencing of Brevibacterium sediminis MG-1 isolate with growth-promoting properties. 3 Biotech 2022; 12:326. [PMID: 36276447 PMCID: PMC9576829 DOI: 10.1007/s13205-022-03392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/29/2022] [Indexed: 11/01/2022] Open
Abstract
In recent years, plant growth-promoting rhizobacteria (PGPR) have received increased attention due to their prospective use as biofertilizers for the enhancement of crop growth and yields. However, there is a growing need to identify new PGPR isolates with additional beneficial properties. In this paper, we describe the identification of a new strain of a non-sporulating Gram-positive bacterium isolated from the rhizosphere of potato plants, classified as Brevibacterium sediminis MG-1 based on whole-genome sequencing. The bacteria are aerobic; they grow in a pH range of 6.0-10.0 (optimum 6.0), and a temperature range of 20-37 °C (optimum 30 °C). At 96 h of cultivation, strain MG-1 synthesizes 28.65 µg/ml of indole-3-acetic acid (IAA) when 500 µg/ml of l-tryptophan is added. It is a producer of catechol-type siderophores and ACC deaminase (213 ± 12.34 ng/ml) and shows halotolerance. Treatment of pea, rye, and wheat seeds with a suspension of MG-1 strain cells resulted in the stimulation of stem and root biomass accumulation by 12-26% and 6-25% (P < 0.05), respectively. Treatment of seeds with bacteria in the presence of high salt concentration reduced the negative effects of salt stress on plant growth by 18-50%. The hypothetical gene lin, encoding the bacteriocin Linocin-M18, RIPP-like proteins, and polyketide synthase type III (T3PKS) loci, gene clusters responsible for iron acquisition and metabolism of siderophores, as well as gene clusters responsible for auxin biosynthesis, were identified in the B. sediminis MG-1 genome. Thus, the rhizosphere-associated strain B. sediminis MG-1 has growth-stimulating properties and can be useful for the treatment of plants grown on soils with high salinity. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03392-z.
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Affiliation(s)
- Marat Tafkilevich Lutfullin
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
- Laboratory of Agrobioengineering, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
| | - Guzel Fanisovna Lutfullina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
- Laboratory of Agrobioengineering, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
| | - Dasha Sergeevna Pudova
- Laboratory of Agrobioengineering, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
| | - Yaw Abayie Akosah
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, USA
| | - Elena Ilyasovna Shagimardanova
- Research Center Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
| | - Semyon Germanovich Vologin
- Department of Breeding and Biotechnology of Potatoes, Tatar Research Institute of Agriculture, Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, Kazan, Russia
| | - Margarita Rashidovna Sharipova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
- Laboratory of Agrobioengineering, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
| | - Ayslu Mirkasymovna Mardanova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
- Laboratory of Agrobioengineering, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia
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Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress. Mol Cell Proteomics 2022; 21:100423. [PMID: 36210010 PMCID: PMC9650054 DOI: 10.1016/j.mcpro.2022.100423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/09/2022] Open
Abstract
Organisms have developed different mechanisms to respond to stresses. However, the roles of small ORF-encoded peptides (SEPs) in these regulatory systems remain elusive, which is partially because of the lack of comprehensive knowledge regarding these biomolecules. We chose the extremophile Deinococcus radiodurans R1 as a model species and conducted large-scale profiling of the SEPs related to the stress response. The integrated workflow consisting of multiple omics approaches for SEP identification was streamlined, and an SEPome of D. radiodurans containing 109 novel and high-confidence SEPs was drafted. Forty-four percent of these SEPs were predicted to function as antimicrobial peptides. Quantitative peptidomics analysis indicated that the expression of SEP068184 was upregulated upon oxidative treatment and gamma irradiation of the bacteria. SEP068184 was conserved in Deinococcus and exhibited negative regulation of oxidative stress resistance in a comparative phenotypic assay of its mutants. Further quantitative and interactive proteomics analyses suggested that SEP068184 might function through metabolic pathways and interact with cytoplasmic proteins. Collectively, our findings demonstrate that SEPs are involved in the regulation of oxidative resistance, and the SEPome dataset provides a rich resource for research on the molecular mechanisms of the response to extreme stress in organisms.
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Robiginitalea marina sp. nov., isolated from coastal sediment. Arch Microbiol 2022; 204:644. [PMID: 36163309 DOI: 10.1007/s00203-022-03263-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative, orange, aerobic, non-motile, rod-shaped marine bacterium, designated as 2V75T, was isolated from the coastal sediment of Xiaoshi Island, Weihai, China. The strain 2V75T grew at 20-45 °C (optimum, 37 °C), from pH 7.0 to 9.0 (optimum, pH 7.0) and in the presence of 0.5-5% (w/v) NaCl (optimum, 3%). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain 2V75T was affiliated to the genus Robiginitalea and had the highest sequence similarity with R. biformata KCTC 12146T (93.7%). The ANI values between strain 2V75T and R. biformata KCTC 12146T were 72.6%, respectively. The DNA G + C content was 54.8 mol%. MK-6 was the only respiratory quinone. Based on the phenotypic, phylogenetic and chemotaxonomic data, strain 2V75T should be classified as a novel species in the genus Robiginitalea, for which the name Robiginitalea marina is proposed. The type strain is 2V75T (= KCTC 92035T = MCCC 1H00484T).
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Boss BL, Wanees AE, Zaslow SJ, Normile TG, Izquierdo JA. Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata. BMC Genomics 2022; 23:508. [PMID: 35831788 PMCID: PMC9281055 DOI: 10.1186/s12864-022-08738-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4. Results Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms. Conclusion The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08738-8.
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Affiliation(s)
- Brianna L Boss
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Abanoub E Wanees
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Shari J Zaslow
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Tyler G Normile
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
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Lysobacter chinensis sp. nov., a cellulose-degrading strain isolated from cow dung compost. Antonie Van Leeuwenhoek 2022; 115:1031-1040. [PMID: 35699855 DOI: 10.1007/s10482-022-01755-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/21/2022] [Indexed: 10/18/2022]
Abstract
A novel bacterial strain, TLK-CK17T, was isolated from cow dung compost sample. The strain was Gram-staining negative, non-gliding rods, aerobic, and displayed growth at 15-40 °C (optimally, 35 °C), with 0-5.0% (w/v) NaCl (optimally, 0.5) and at pH 6.5-8.5 (optimally, 7.0-7.5). The assembled genome of strain TLK-CK17T has a total length of 4.3 Mb with a G + C content of 68.2%. According to the genome analysis, strain TLK-CK17T encodes quite a few glycoside hydrolases that may play a role in the degradation of accumulated plant biomass in compost. On the basis 16S rRNA gene sequence analysis, strain TLK-CK17T showed the highest sequence similarity (98.9%) with L. penaei GDMCC 1.1817 T, followed by L. maris KCTC 42381 T (98.3%). Cells contained iso-C16:0, iso-C15:0, and summed feature 9 (comprising C17:1 ω9c and/or 10-methyl C16:0), as its major cellular fatty acids (> 10.0%) and ubiquinone-8 as the exclusively respiratory quinone. Diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol prevailed among phospholipids. Based on the phenotypic, genomic and phylogenetic data, strain TLK-CK17T represents a novel species of the genus Lysobacter, for which the name Lysobacter chinensis sp. nov. is proposed, and the type strain is TLK-CK17T (= CCTCC AB2021257T = KCTC 92122 T).
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Scarduelli M, Guizelini D, Alves Cardos RL, Ceccon DM, Donatti L, de Baura VA, de Oliveira Pedrosa F, Huergo LF, de Souza EM. The Complete Genome Sequence of Bacillus safensis BRM1 Isolated from Brazilian Mangrove Sediment: A Potential Source of Biomass Converting Enzymes. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2203180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
Bacillus safensis BRM1 was isolated from Brazilian mangrove sediment and selected for its ability to grow in xylan as the sole carbon source. To identify genes encoding biomass conversion enzymes, the genome of this bacterium was sequenced.
Methods:
Genome wide analysis revealed 99% nucleotide identity to the Bacillus safensis genome. The isolated strain was named B. safensis BRM1, and its genome consists of a circular chromosome of 3.74 Mb with a GC content of 41.8%. Genes encoding a plethora of hydrolytic enzymes are present in the BRM1 genome but absent from the other B. safensis genomes.
Results:
A total of 23 genes encoding putative cellulases or hemicellulases were identified.
Conclusion:
These data support that B. safensis BRM1 is an interesting candidate for the prospection of enzymes that can be applied in the conversion of cellulosic biomass to biofuel.
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Oceanisphaera pacifica sp. nov., isolated from the intestine of Trichiurus japonicus. Arch Microbiol 2022; 204:338. [PMID: 35590019 DOI: 10.1007/s00203-022-02928-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 04/17/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative, strictly aerobic, non-flagellated, oxidase- and catalase-positive, rod-shaped marine bacterium, designated strain DM8T, was isolated from the intestine of Trichiurus japonicus in Weihai, China. The strain optimally grew at 25-35℃, with 1.0-4.0% (w/v) NaCl and at pH 7.0-8.0. Its colonies were circular, slightly yellow, non-transparent, smooth, and approximately 0.8-1.5 mm in diameter, after being cultured for 48 h on marine agar 2216. Based on the result of phylogenetic analysis of 16S rRNA gene sequence, strain DM8T had close relationship with Oceanisphaera profunda SM1222T (96.9%) and the type strain DSM 15406 T of the type species Oceanisphaera litoralis (94.7%), respectively. Genome sequencing revealed a genome size of 3,109,059 bp and a G + C content of 46.9 mol%. It had Q-8 as the sole respiratory quinone and possessed C16:0, summed features 3 (C16:1ω7c/C16:1ω6c) and summed features 8 (C18:1ω7c/C18:1ω6c) as major fatty acids. The major polar lipid profile was composed of phosphatidylglycerol and phosphatidylethanolamine. Based on the phenotypic, chemotaxonomic characterizations, phylogenetic properties and genome analysis, strain DM8T should represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera pacifica sp. nov. is proposed. The type strain is DM8T (= KCTC 82764 T = MCCC 1K06133T).
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Psychroserpens luteolus sp. nov., isolated from Gelidium, reclassification of Ichthyenterobacterium magnum as Psychroserpens magnus comb. nov., Flavihalobacter algicola as Psychroserpens algicola comb. nov., Arcticiflavibacter luteus as Psychroserpens luteus comb. nov. Arch Microbiol 2022; 204:279. [DOI: 10.1007/s00203-022-02895-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
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Abstract
The phylum "Candidatus Omnitrophica" (candidate division OP3) is ubiquitous in anaerobic habitats but is currently characterized only by draft genomes from metagenomes and single cells. We had visualized cells of the phylotype OP3 LiM in methanogenic cultures on limonene as small epibiotic cells. In this study, we enriched OP3 cells by double density gradient centrifugation and obtained the first closed genome of an apparently clonal OP3 cell population by applying metagenomics and PCR for gap closure. Filaments of acetoclastic Methanosaeta, the largest morphotype in the culture community, contained empty cells, cells devoid of rRNA or of both rRNA and DNA, and dead cells according to transmission electron microscopy (TEM), thin-section TEM, scanning electron microscopy (SEM), catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), and LIVE/DEAD imaging. OP3 LiM cells were ultramicrobacteria (200 to 300 nm in diameter) and showed two physiological stages in CARD-FISH fluorescence signals: strong signals of OP3 LiM cells attached to Bacteria and to Archaea indicated many rRNA molecules and an active metabolism, whereas free-living OP3 cells had weak signals. Metaproteomics revealed that OP3 LiM lives with highly expressed secreted proteins involved in depolymerization and uptake of macromolecules and an active glycolysis and energy conservation by the utilization of pyruvate via a pyruvate:ferredoxin oxidoreductase and an Rnf complex (ferredoxin:NAD oxidoreductase). Besides sugar fermentation, a nucleotidyl transferase may contribute to energy conservation by phosphorolysis, the phosphate-dependent depolymerization of nucleic acids. Thin-section TEM showed distinctive structures of predation. Our study demonstrated a predatory metabolism for OP3 LiM cells, and therefore, we propose the name "Candidatus Velamenicoccus archaeovorus" gen. nov., sp. nov., for OP3 LiM. IMPORTANCE Epibiotic bacteria are known to live on and off bacterial cells. Here, we describe the ultramicrobacterial anaerobic epibiont OP3 LiM living on Archaea and Bacteria. We detected sick and dead cells of the filamentous archaeon Methanosaeta in slowly growing methanogenic cultures. OP3 LiM lives as a sugar fermenter, likely on polysaccharides from outer membranes, and has the genomic potential to live as a syntroph. The predatory lifestyle of OP3 LiM was supported by its genome, the first closed genome for the phylum "Candidatus Omnitrophica," and by images of cell-to-cell contact with prey cells. We propose naming OP3 LiM "Candidatus Velamenicoccus archaeovorus." Its metabolic versatility explains the ubiquitous presence of "Candidatus Omnitrophica" 3 in anoxic habitats and gives ultramicrobacterial epibionts an important role in the recycling and remineralization of microbial biomass. The removal of polysaccharides from outer membranes by ultramicrobacteria may also influence biological interactions between pro- and eukaryotes.
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Draft Genome Sequences of Sixteen Fluoroquinolone-Resistant Extraintestinal Escherichia coli Isolates from Human Patients. Microbiol Resour Announc 2022; 11:e0000322. [PMID: 35289649 PMCID: PMC9022563 DOI: 10.1128/mra.00003-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here the draft genome sequences of 16 fluoroquinolone-resistant extraintestinal Escherichia coli isolates from human patients. These isolates had high MICs (32 to 256 μg/mL) for ciprofloxacin and contained point mutations in the quinolone resistance-determining region (QRDR) of both gyrA and parC that confer resistance to fluoroquinolone. The whole-genome sequence data provide a better understanding of the fluoroquinolone resistance mechanisms in these isolates and would be beneficial in source tracking these pathogens during pandemic outbreaks.
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Reoccurring bovine anthrax in Germany on the same pasture after 12 years. J Clin Microbiol 2022; 60:e0229121. [PMID: 35195442 PMCID: PMC8925895 DOI: 10.1128/jcm.02291-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The zoonotic disease anthrax, caused by the endospore-forming bacterium Bacillus anthracis, is very rare in Germany. In the state of Bavaria, the last case occurred in July of 2009, resulting in four dead cows. In August of 2021, the disease reemerged after heavy rains, killing one gestating cow. Notably, both outbreaks affected the same pasture, suggesting a close epidemiological connection. B. anthracis could be grown from blood culture, and the presence of both virulence plasmids (pXO1 and pXO2) was confirmed by PCR. Also, recently developed diagnostic tools enabled rapid detection of B. anthracis cells and nucleic acids directly in clinical samples. The complete genome of the strain isolated from blood, designated BF-5, was DNA sequenced and phylogenetically grouped within the B.Br.CNEVA clade, which is typical for European B. anthracis strains. The genome was almost identical to BF-1, the isolate from 2009, separated only by three single nucleotide polymorphisms (SNPs) on the chromosome, one on plasmid pXO2 and three indel regions. Further, B. anthracis DNA was detected by PCR from soil samples taken from spots in the pasture where the cow had fallen. New tools based on phage receptor-binding proteins enabled the microscopic detection and isolation of B. anthracis directly from soil samples. These environmental isolates were genotyped and found to be identical to BF-5 in terms of SNPs. Therefore, it seems that the BF-5 genotype is currently the prevalent one at the affected premises. The area contaminated by the cadaver was subsequently disinfected with formaldehyde.
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Chaplin AV, Shcherbakova VA, Pikina AP, Sokolova SR, Korzhanova M, Belova VA, Korostin DO, Rebrikov DV, Kardonsky DA, Urban AS, Zakharzhevskaya NB, Suzina NE, Podoprigora IV, Das MS, Kholopova DO, Efimov BA. Diplocloster agilis gen. nov., sp. nov. and Diplocloster modestus sp. nov., two novel anaerobic fermentative members of Lachnospiraceae isolated from human faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005222] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Three novel strains of Gram-stain-negative, obligately anaerobic, spore-forming straight or slightly curved rods with pointed ends occurring singly or in pairs were isolated from the faeces of healthy human children. The strains were characterized by mesophilic fermentative metabolism and production of acetate, ethanol and H2 as the end metabolic products. Strains ASD3451 and ASD5720T were motile, fermented lactose and raffinose, and weakly fermented maltose. Strain ASD4241T was non-motile and did not ferment the carbohydrates listed above but fermented starch. Strains ASD3451 and ASD5720T shared average nucleotide identity higher than 98.5 % with each other, while ASD4241T had only 88.5-89 % identity to them. Based on phylogenetic and chemotaxonomic analyses, we propose Diplocloster agilis gen. nov., sp. nov. (ASD5720T=JCM 34353T=VKM B-3497T) and Diplocloster modestus sp. nov. (ASD4241T=JCM 34351T=VKM B-3498T) within the family
Lachnospiraceae
.
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Affiliation(s)
- Andrei V. Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoria A. Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Alla P. Pikina
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofia R. Sokolova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Margarita Korzhanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry A. Kardonsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Anatoly S. Urban
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia B. Zakharzhevskaya
- Federal Research and Clinical Centre of Physical-Chemical Medicine Federal Medical Biological Agency, Moscow, Russia
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research, Russian Academy of Sciences”, Pushchino, Russia
| | - Irina V. Podoprigora
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Milana S. Das
- Department of Microbiology and Virology, Peoples' Friendship University of Russia, Moscow, Russia
| | - Daria O. Kholopova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris A. Efimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
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Petrigna L, Karsten B, Delextrat A, Pajaujiene S, Mani D, Paoli A, Palma A, Bianco A. An updated methodology to estimate critical velocity in front crawl swimming: A scoping review. Sci Sports 2022. [DOI: 10.1016/j.scispo.2021.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Petrigna L, Thomas E, Scardina A, Rizzo F, Brusa J, Camarazza G, Galassi C, Palma A, Bellafiore M. Methodological Considerations for Movement Education Interventions in Natural Environments for Primary School Children: A Scoping Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031505. [PMID: 35162531 PMCID: PMC8835137 DOI: 10.3390/ijerph19031505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 01/28/2023]
Abstract
Background: Education is the ideal setting for carrying out projects to improve primary students’ capacities. In recent years, interventions in natural environments have been more frequently proposed, but there is still a lack of standardization, making deeper study of the topic necessary. This review aims to report on what previous scientific research has been carried out, and eventually, to propose standard operating procedures for future interventions. Methods: This is a scoping review that adopted the PRISMA guidelines. Primary school children have been included, and the interventions had to be proposed adopting nature as the primary element of the learning process. Results: A total of 19 studies have been included, and a wide range of methodological differences has been detected regarding the included intervention protocols. Conclusions: Learning in nature is a feasible intervention that, despite the high heterogeneity of interventions, demonstrates positive outcomes in the learning sphere of children.
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Affiliation(s)
- Luca Petrigna
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
- Correspondence:
| | - Ewan Thomas
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
| | - Antonino Scardina
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
| | - Federica Rizzo
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
| | - Jessica Brusa
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
| | - Giovanni Camarazza
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
- Regional School Office of Sicily (USR Sicilia), Via San Lorenzo Colli n° 312/g, 90146 Palermo, Italy
| | - Claudia Galassi
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
- Regional School Office of Sicily (USR Sicilia), Via San Lorenzo Colli n° 312/g, 90146 Palermo, Italy
| | - Antonio Palma
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
| | - Marianna Bellafiore
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (E.T.); (A.S.); (F.R.); (J.B.); (G.C.); (C.G.); (A.P.); (M.B.)
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Quintas-Nunes F, Rossi MJ, Nascimento FX. Genomic insights into the plant-associated lifestyle of Kosakonia radicincitans MUSA4, a diazotrophic plant-growth-promoting bacterium. Syst Appl Microbiol 2022; 45:126303. [DOI: 10.1016/j.syapm.2022.126303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/06/2022] [Accepted: 01/18/2022] [Indexed: 11/27/2022]
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Fuertes-Perez S, Vogel RF, Hilgarth M. Comparative genomics of Photobacterium species from terrestrial and marine habitats. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100087. [PMID: 34950912 PMCID: PMC8671102 DOI: 10.1016/j.crmicr.2021.100087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/26/2021] [Indexed: 11/28/2022] Open
Abstract
Photobacterium (P.) is a genus widely studied in regards to its association with and ubiquitous presence in marine environments. However, certain species (P. phosphoreum, P. carnosum, P. iliopiscarium) have been recently described to colonize and spoil raw meats without a marine link. We have studied 27 strains from meat as well as 26 strains from marine environments in order to probe for intraspecies marine/terrestrial subpopulations and identify distinct genomic features acquired by environmental adaptation. We have conducted phylogenetic analysis (MLSA, ANI, fur, codon usage), search of plasmids (plasmidSPADES), phages (PHASTER), CRISPR-cas operons (CRISPR-finder) and secondary metabolites gene clusters (antiSMASH, BAGEL), in addition to a targeted gene search for specific pathways (e.g. TCA cycle, pentose phosphate, respiratory chain) and elements relevant for growth, adaptation and competition (substrate utilization, motility, bioluminescence, sodium and iron transport). P. carnosum appears as a conserved single clade, with one isolate from MAP fish clustering apart that doesn't, however, show distinct features that could indicate different adaptation. The species harbors genes for a wide carbon source utilization (glycogen/starch, maltose, pullulan, fucose) for colonization of diverse niches in its genome. P. phosphoreum is represented by two different clades on the phylogenetic analyses not correlating to their origin or distribution of other features analyzed that can be divided into two novel subspecies based on genome-wide values. A more diverse antimicrobial activity (sactipeptides, microcins), production of secondary metabolites (siderophores and arylpolyenes), stress response and adaptation (bioluminescence, sodium transporters, catalase, high affinity for oxygen cytochrome cbb3 oxidase, DMSO reductase and proton translocating NADH dehydrogenase) is predicted compared to the other species. P. iliopiscarium was divided into two clades based on source of isolation correlating with phylogeny and distribution of several traits. The species shows traits common to the other two species, similar carbon utilization/transport gene conservation as P. carnosum for the meat-isolated strains, and predicted utilization of marine-common DMSO and flagellar cluster for the sea-isolated strains. Results additionally suggest that photobacteria are highly prone to horizontal acquisition/loss of genetic material and genetic transduction, and that it might be a strategy for increasing the frequency of strain- or species-specific features that offers a growth/competition advantage.
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Affiliation(s)
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Germany
| | - Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Germany
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34
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The importance of standard operating procedures in physical fitness assessment: a brief review. SPORT SCIENCES FOR HEALTH 2021. [DOI: 10.1007/s11332-021-00849-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Abstract
Background
Physical fitness status is a key aspect of health and, consequently, it is important to create and adopt appropriate interventions to maintain or improve it, and assess it using valid measures. While in other testing contexts, standard operating procedures (SOPs) are commonly and widely adopted, in physical fitness testing, a variety of unstandardized testing protocols are proposed.
Aims
The topic of this review was to evaluate the existing literature on SOPs in physical fitness assessment and to provide guidelines on how SOPs could be created and adopted.
Method
The electronic databases PubMed, Web of Science and Scopus were screened and original, peer-reviewed studies that included SOPs, related to physical fitness, were recorded.
Results
After the inclusion and exclusion criteria screening, a total of six studies were included and these were critically and narratively analyzed.
Conclusions
Standard operating procedures are rarely adopted in the field of physical fitness and a step by step guide has been provided in this manuscript. In the future, it is suggested to follow protocols as a routine, because this is the only way to generalize and contextualize findings.
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Nascimento FX, Urón P, Glick BR, Giachini A, Rossi MJ. Genomic Analysis of the 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Pseudomonas thivervalensis SC5 Reveals Its Multifaceted Roles in Soil and in Beneficial Interactions With Plants. Front Microbiol 2021; 12:752288. [PMID: 34659189 PMCID: PMC8515041 DOI: 10.3389/fmicb.2021.752288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Beneficial 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing bacteria promote plant growth and stress resistance, constituting a sustainable alternative to the excessive use of chemicals in agriculture. In this work, the increased plant growth promotion activity of the ACC deaminase-producing Pseudomonas thivervalensis SC5, its ability to limit the growth of phytopathogens, and the genomics behind these important properties are described in detail. P. thivervalensis SC5 displayed several active plant growth promotion traits and significantly increased cucumber plant growth and resistance against salt stress (100mmol/L NaCl) under greenhouse conditions. Strain SC5 also limited the in vitro growth of the pathogens Botrytis cinerea and Pseudomonas syringae DC3000 indicating active biological control activities. Comprehensive analysis revealed that P. thivervalensis SC5 genome is rich in genetic elements involved in nutrient acquisition (N, P, S, and Fe); osmotic stress tolerance (e.g., glycine-betaine, trehalose, and ectoine biosynthesis); motility, chemotaxis and attachment to plant tissues; root exudate metabolism including the modulation of plant phenolics (e.g., hydroxycinnamic acids), lignin, and flavonoids (e.g., quercetin); resistance against plant defenses (e.g., reactive oxygens species-ROS); plant hormone modulation (e.g., ethylene, auxins, cytokinins, and salicylic acid), and bacterial and fungal phytopathogen antagonistic traits (e.g., 2,4-diacetylphloroglucinol, HCN, a fragin-like non ribosomal peptide, bacteriocins, a lantipeptide, and quorum-quenching activities), bringing detailed insights into the action of this versatile plant-growth-promoting bacterium. Ultimately, the combination of both increased plant growth promotion/protection and biological control abilities makes P. thivervalensis SC5 a prime candidate for its development as a biofertilizer/biostimulant/biocontrol product. The genomic analysis of this bacterium brings new insights into the functioning of Pseudomonas and their role in beneficial plant-microbe interactions.
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Affiliation(s)
- Francisco X Nascimento
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,Laboratório de Microbiologia e Bioprocessos, Departamento de Microbiologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Paola Urón
- Laboratório de Microbiologia e Bioprocessos, Departamento de Microbiologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Admir Giachini
- Laboratório de Microbiologia e Bioprocessos, Departamento de Microbiologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Márcio J Rossi
- Laboratório de Microbiologia e Bioprocessos, Departamento de Microbiologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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A Combination of Genomics, Transcriptomics, and Genetics Provides Insights into the Mineral Weathering Phenotype of Pseudomonas azotoformans F77. Appl Environ Microbiol 2021; 87:e0155221. [PMID: 34586903 DOI: 10.1128/aem.01552-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Silicate mineral weathering (dissolution) plays important roles in soil formation and global biogeochemical cycling. In this study, a combination of genomics, transcriptomics, and genetics was used to identify the molecular basis of mineral weathering activity and acid tolerance in Pseudomonas azotoformans F77. Biotite was chosen as a silicate mineral to investigate mineral weathering. The genome of strain F77 was sequenced, and the genes significantly upregulated when grown in the presence of biotite included mineral weathering-related genes associated with gluconic acid metabolism, flagellar assembly, and pilus biosynthesis and acid tolerance-related genes associated with neutralizing component production, reducing power, and proton efflux. Then, the biotite-weathering behaviors of strain F77 and its mutants that were created by deleting the tkt, tal, gntP, potF, nuoF, and gdtO genes, which are involved in gluconic acid metabolism and acid tolerance, respectively, were determined. The Fe and Al concentrations in the strain F77-inoculated medium increased 2.2- to 13.7-fold compared to the controls. The cell numbers of strain F77 increased over time, while the pH values in the medium ranged from 3.75 to 3.90 between 20 and 36 h of incubation. The release of Al and Fe was significantly reduced in the mutants F77Δtal, F77ΔgntP, F77ΔpotF, and F77ΔnuoF. Bacterial growth was significantly reduced in the presence of biotite in the mutants F77ΔpotF and F77ΔnuoF. Our results demonstrated the acid tolerance of strain F77 and suggested that multiple genes and metabolic pathways in strain F77 are involved in biotite weathering and acid tolerance during the mineral weathering process. IMPORTANCE Acid production and tolerance play important roles in effective and persistent mineral weathering in bacteria, although the molecular mechanisms governing acid production and acid tolerance in bacteria have not been fully elucidated. In this study, the molecular mechanisms underlying biotite (as a silicate mineral) weathering (dissolution) and acid tolerance of P. azotoformans F77 were characterized using genomics, transcriptomics, and genetics analyses. Our results showed that the genes and metabolic pathways for gluconic acid metabolism, flagellar assembly, and pilus biosynthesis may play important roles in mineral weathering by strain F77. Notably, the genes associated with neutralizing component production, reducing power, and proton efflux may be related to acid tolerance in strain F77. The expression of these acid production- and acid tolerance-related genes was observed to be increased by biotite in strain F77. Our findings may help to elucidate the molecular mechanisms governing mineral weathering and, especially, acid tolerance in mineral-weathering bacteria.
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Yue Q, Zhang Q, Wang Y, He X, Ding K, Wang X, Xi H, Wang L, Zhang Y, Wu C. Complete genome sequencing and comparative analysis of Citrobacter koseri CKNJ, a strain isolated from patient with endogenous endophthalmitis. Jpn J Infect Dis 2021; 75:148-155. [PMID: 34470967 DOI: 10.7883/yoken.jjid.2021.334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Citrobacter koseri is an opportnistic pathogen can cause a variety of diseases. Though the mortality rate of C. koseri infections is high but there is a paucity of clinical information on them. Furthermore, the genomic features of this species are poorly studied. Herein, we presented a patient with endogenous endophthalmitis secondary to septicaemia, and collected a C. koseri isolate, CKNJ, from the blood of the patient. Whole genome sequencing revealed that the CKNJ harbors no plasmid and codes for 67 putative virulence factors. Whole genome SNP-based phylogenetic analysis revealed that strain CKNJ was close to the strains with same isolation sites. Compared to the other sequenced C. koseri chromosomes, CKNJ contains several strain-variable regions, including one prophage and two large genomic islands. The sequencing of the first complete genome of a clinical strain from China should reinforce our understanding of the genomic features and pathogenicity of this invasive infection-causing C. koseri with clinical significance.
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Affiliation(s)
- Qiaoyan Yue
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, China.,Department of Infectious Diseases, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Qiyue Zhang
- Department of Infectious Diseases, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Yueqin Wang
- Department of Infectious Diseases, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Xiaoju He
- Department of Infectious Diseases, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Kang Ding
- National Center of Colorectal Surgery, Jiangsu Integrate Colorectal Oncology Center, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Xiaofeng Wang
- National Center of Colorectal Surgery, Jiangsu Integrate Colorectal Oncology Center, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Haiyan Xi
- Department of Medical Laboratory, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Lulu Wang
- Department of Medical Laboratory, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Yanliang Zhang
- Department of Infectious Diseases, the Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, China
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, China
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38
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Newstead LL, Harris J, Goodbrand S, Varjonen K, Nuttall T, Paterson GK. Staphylococcus caledonicus sp. nov. and Staphylococcus canis sp. nov. isolated from healthy domestic dogs. Int J Syst Evol Microbiol 2021; 71. [PMID: 34296985 PMCID: PMC8489841 DOI: 10.1099/ijsem.0.004878] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Two strains, H8/1T and H16/1AT, of Gram-stain-positive, coagulase-negative staphylococci were isolated from separate healthy domestic dogs in Scotland. Both strains were genome sequenced and their inferred DNA–DNA hybridisation indicates that H8/1T and H16/1AT represent two novel species of the genus Staphylococcus. On the basis of the results of genome sequence analysis (genome blast distance phylogeny and single nucleotide polymorphism analysis) H8/1T is most closely related to Staphylococcus devriesei and H16/1AT most closely related to Staphylococcus felis. Also, average nucleotide identity distinguished H8/1T and H16/1AT from S. devriesei and S. felis as did minor phenotypic differences. On the basis of these results, it is proposed that H8/1T and H16/1AT represent novel species with the respective names Staphylococcus caledonicus and Staphylococcus canis. The type strain of S. caledonicus is H8/1T (=NCTC 14452T=CCUG 74789T). The type strain of S. canis is H16/1AT (=NCTC 14451T=CCUG 74790T)
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Affiliation(s)
- Logan L Newstead
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - J Harris
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - S Goodbrand
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - K Varjonen
- AniCura Djursjukhuset Albano, Rinkebyvägen 21A, 182 36 Danderyd, Sweden
| | - T Nuttall
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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39
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Zhou J, Zhang S, Zhang G, Yang J, Lai XH, Pu J, Jin D, Lu S, Huang Y, Zhu W, Huang Y, Xu M, Lei W, Cheng Y, Liu L, Xu J. Characterization of isolates of members of the genus Actinomyces from Marmota himalayana: description of Actinomyces faecalis sp. nov., Actinomyces respiraculi sp. nov., and Actinomyces trachealis sp. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34252022 DOI: 10.1099/ijsem.0.004875] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six novel strains (ZJ34T, ZJ561, ZJ750T, ZJ1629, zg-993T and zg-987) isolated from faeces and respiratory tracts of Marmota himalayana from the Qinghai-Tibet Plateau of PR China were characterized comprehensively. The results of analyses of the 16S rRNA gene and genome sequences indicated that the six strains represent three novel species of the genus Actinomyces, and are closely related to Actinomyces urogenitalis DSM 15434T (16S rRNA gene sequences similarities, 94.9-98.7 %), Actinomyces weissii CCUG 61299T (95.6-96.6 %), Actinomyces bovis CCTCC AB2010168T (95.7 %) and Actinomyces bowdenii DSM 15435T (95.2-96.4 %), with values of digital DNA-DNA hybridization less than 30.1 % when compared with their closest relatives but higher than 70 % within each pair of novel strains (ZJ34T/ZJ561, ZJ750T/ZJ1629 and zg-993T/zg-987). All the novel strains had C18 : 1 ω9c and C16 : 0 as the two most abundant major fatty acids. MK-9(H4) or MK-8(H4) was the sole or predominant respiratory quinone of strains ZJ34T, ZJ750T and zg-993T and their polar lipid profiles differed, but all had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidyl inositol mannoside as major components. ZJ750T shared identical peptidoglycan amino acid profile with ZJ34T (alanine, glutamic acid, lysine and ornithine) and the same whole-cell sugar composition with zg-993T (glucose, rhamnose and ribose). Strain zg-993T contained alanine, aspartic acid, glutamic acid, glycine and lysine in the peptidoglycan, and the only sugar in ZJ34T was ribose. The DNA G+C contents of the novel strains were within the range of 65.8-70.1 mol%. On the basis of the results from the aforementioned analyses, the six novel strains were classified as representing three novel species of genus Actinomyces, for which the names Actinomyces faecalis sp. nov. [type strain ZJ34T (=GDMCC 1.1952T=JCM 34355T)], Actinomyces respiraculi sp. nov. [type strain ZJ750T (=GDMCC 1.1950T=JCM 34356T)] and Actinomyces trachealis sp. nov. [type strain zg-993T (=GDMCC 1.1956T=JCM 34357T)] were proposed, respectively.
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Affiliation(s)
- Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Sihui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing 100191, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, Henan Province, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Mingchao Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu Province, PR China
| | - Wenjing Lei
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi Province, PR China
| | - Yanpeng Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi Province, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Research Institute of Public Health, Nankai University, Tianjin 300350, PR China
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40
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Zhu KL, Wang XQ, Zhang TS, Shang DD, Du ZJ. Salibaculum halophilum gen. nov., sp. nov. and Salibaculum griseiflavum sp. nov., in the family Rhodobacteraceae. Int J Syst Evol Microbiol 2021; 71. [PMID: 34170216 DOI: 10.1099/ijsem.0.004808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, moderately halophilic, non-motile, rod-shaped, pale yellow, and aerobic strains, designated WDS1C4T and WDS4C29T, were isolated from a marine solar saltern in Weihai, Shandong Province, PR China. Growth of strain WDS1C4T occurred at 10-45 °C (optimum, 37 °C), with 4-16 % (w/v) NaCl (optimum, 8 %) and at pH 6.5-9.0 (optimum, pH 7.5). Growth of strain WDS4C29T occurred at 10-45 °C (optimum, 40 °C), with 2-18 % (w/v) NaCl (optimum, 6 %) and at pH 6.5-9.0 (optimum, pH 7.5). Q-10 was the sole respiratory quinone of the two strains. The major polar lipids of strains WDS1C4T and WDS4C29T were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major cellular fatty acid in strains WDS1C4T and WDS4C29T was C18 : 1 ω7c, and the genomic DNA G+C contents of strains WDS1C4T and WDS4C29T were 67.6 and 63.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains WDS1C4T and WDS4C29T were members of the family Rhodobacteraceae and showed 94.3 and 95.3 % similarities to their closest relative, Celeribacter indicus, respectively. The similarity between WDS1C4T and WDS4C29T was 97.3 %. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing two novel species in a new genus for which the names Salibaculum halophilum gen. nov., sp. nov. (type species, type strain WDS1C4T=MCCC 1H00179T=KCTC 52542T) and Salibaculum griseiflavum sp. nov. (WDS4C29T=MCCC 1H00175T=KCTC 52541T) are proposed.
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Affiliation(s)
- Ke-Lei Zhu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xiao-Qun Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Tian-Shu Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
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41
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Antequera‐Gómez ML, Díaz‐Martínez L, Guadix JA, Sánchez‐Tévar AM, Sopeña‐Torres S, Hierrezuelo J, Doan HK, Leveau JH, de Vicente A, Romero D. Sporulation is dispensable for the vegetable-associated life cycle of the human pathogen Bacillus cereus. Microb Biotechnol 2021; 14:1550-1565. [PMID: 33955675 PMCID: PMC8313275 DOI: 10.1111/1751-7915.13816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/18/2021] [Accepted: 04/03/2021] [Indexed: 11/28/2022] Open
Abstract
Bacillus cereus is a common food-borne pathogen that is responsible for important outbreaks of food poisoning in humans. Diseases caused by B. cereus usually exhibit two major symptoms, emetic or diarrheic, depending on the toxins produced. It is assumed that after the ingestion of contaminated vegetables or processed food, spores of enterotoxigenic B. cereus reach the intestine, where they germinate and produce the enterotoxins that are responsible for food poisoning. In our study, we observed that sporulation is required for the survival of B. cereus in leaves but is dispensable in ready-to-eat vegetables, such as endives. We demonstrate that vegetative cells of B. cereus that are originally impaired in sporulation but not biofilm formation are able to reach the intestine and cause severe disorders in a murine model. Furthermore, our findings emphasise that the number of food poisoning cases associated with B. cereus is underestimated and suggest the need to revise the detection protocols, which are based primarily on spores and toxins.
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Affiliation(s)
- María Luisa Antequera‐Gómez
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"Universidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Universidad de MálagaBulevar Louis Pasteur 31 (Campus Universitario de teatinos)Málaga29071Spain
| | - Luis Díaz‐Martínez
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"Universidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Universidad de MálagaBulevar Louis Pasteur 31 (Campus Universitario de teatinos)Málaga29071Spain
| | - Juan Antonio Guadix
- Departamento de Biología AnimalFacultad de CienciasUniversidad de Málaga ‐ IBIMACampus de Teatinos s/nMálaga29071Spain
- Centro Andaluz de Nanomedicina y Biotecnología (BIONAND)Junta de AndalucíaUniversidad de MálagaC/ Severo Ochoa 35Campanillas (Málaga)29590Spain
| | - Ana María Sánchez‐Tévar
- Departamento de Biología AnimalFacultad de CienciasUniversidad de Málaga ‐ IBIMACampus de Teatinos s/nMálaga29071Spain
- Centro Andaluz de Nanomedicina y Biotecnología (BIONAND)Junta de AndalucíaUniversidad de MálagaC/ Severo Ochoa 35Campanillas (Málaga)29590Spain
| | - Sara Sopeña‐Torres
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"Universidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Universidad de MálagaBulevar Louis Pasteur 31 (Campus Universitario de teatinos)Málaga29071Spain
| | - Jesús Hierrezuelo
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"Universidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Universidad de MálagaBulevar Louis Pasteur 31 (Campus Universitario de teatinos)Málaga29071Spain
| | - Hung K. Doan
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | | | - Antonio de Vicente
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"Universidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Universidad de MálagaBulevar Louis Pasteur 31 (Campus Universitario de teatinos)Málaga29071Spain
| | - Diego Romero
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"Universidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Universidad de MálagaBulevar Louis Pasteur 31 (Campus Universitario de teatinos)Málaga29071Spain
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Bartholomäus A, Kolte B, Mustafayeva A, Goebel I, Fuchs S, Benndorf D, Engelmann S, Ignatova Z. smORFer: a modular algorithm to detect small ORFs in prokaryotes. Nucleic Acids Res 2021; 49:e89. [PMID: 34125903 PMCID: PMC8421149 DOI: 10.1093/nar/gkab477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/29/2021] [Accepted: 05/18/2021] [Indexed: 11/15/2022] Open
Abstract
Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use the 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present a new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting putative smORFs. The unique feature of smORFer is that it uses an integrated approach and considers structural features of the genetic sequence along with in-frame translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way, and dependent on the data available for a particular organism, different modules can be selected for smORF search.
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Affiliation(s)
- Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany.,Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Baban Kolte
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Ayten Mustafayeva
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Ingrid Goebel
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | | | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, 39106 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Susanne Engelmann
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Zoya Ignatova
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
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43
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Nascimento FX, Torres CA, Freitas F, Reis MA, Crespo MT. Functional and genomic characterization of Komagataeibacter uvaceti FXV3, a multiple stress resistant bacterium producing increased levels of cellulose. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00606. [PMID: 33747802 PMCID: PMC7970039 DOI: 10.1016/j.btre.2021.e00606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/17/2021] [Accepted: 03/02/2021] [Indexed: 11/29/2022]
Abstract
Bacterial cellulose is one of the most promising biomaterials for the development of a wide array of novel biotechnological solutions. Nevertheless, the commercial production of bacterial cellulose is still a challenge and obtaining novel strains presenting increased cellulose biosynthesis and stress resistance properties is of extreme importance. This work demonstrates the increased stress resistance, cellulose production abilities, and overall genomic properties of Komagataeibacter uvaceti FXV3, a novel cellulose-producing and stress resistant strain isolated from a fermented grape must. K. uvaceti FXV3 was able to grow under several stress conditions, including the presence of high concentrations of ethanol (up to 7.5 % v/v), a trait that is not observed in the model strain K. xylinus CECT 7351T. Moreover, K. uvaceti FXV3 produced increased concentrations of cellulose (4.31 mg/mL, 7 days after inoculation-DAI) when compared to K. xylinus CECT 7351T (1.42 mg/mL, 7 DAI). Moreover, the detailed analysis of strain FXV3 genome revealed the presence of several genes involved in cellulose and acetan biosynthesis, quorum-sensing and quenching mechanisms, carbohydrate, amino acid, alcohol and aldehyde metabolism, as well as several other genes involved in stress resistance. Additionally, comparative genomic analysis revealed the increased prevalence of stress resistance genes in K. uvaceti FXV3 when compared to K. xylinus CECT 7351T. Ultimately, this study reveals the increased biotechnological potential of K. uvaceti FXV3 and brings new insights into the genetics behind Komagataeibacter stress resistance and cellulose production abilities.
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Affiliation(s)
- Francisco X. Nascimento
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
| | - Cristiana A.V. Torres
- UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Filomena Freitas
- UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Maria A.M. Reis
- UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Maria T.B. Crespo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
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44
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Oh YJ, Kim JY, Lim SK, Kwon MS, Choi HJ. Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi. J Microbiol 2021; 59:460-466. [PMID: 33907972 DOI: 10.1007/s12275-021-0513-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 11/25/2022]
Abstract
To date, all species in the genus Salicibibacter have been isolated in Korean commercial kimchi. We aimed to describe the taxonomic characteristics of two strains, NKC5-3T and NKC21-4T, isolated from commercial kimchi collected from various regions in the Republic of Korea. Cells of these strains were rod-shaped, Gram-positive, aerobic, oxidase- and catalase-positive, non-motile, halophilic, and alkalitolerant. Both strains, unlike other species of the genus Salicibibacter, could not grow without NaCl. Strains NKC5-3T and NKC21-4T could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and grow at pH 7.0-10.0 (optimum 8.5) and 8.0-9.0 (optimum 8.5), respectively; they showed 97.1% 16S rRNA gene sequence similarity to each other and were most closely related to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively). The genome of strain NKC5-3T was nearly 4.6 Mb in size, with 4,456 protein-coding sequences (CDSs), whereas NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs. OrthoANI values between the novel strains and S. kimchii NKC1-1T were far lower than the species demarcation threshold. NKC5-3T and NKC21-4T clustered together to form branches that were distinct from the other Salicibibacter species. The major fatty acids in these strains were anteiso-C15:0 and anteiso-C17:0, and the predominant menaquinone was menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and five unidentified phospholipids (PL), and those of NKC21-4T included DPG, PG, seven unidentified PLs, and an unidentified lipid. Both isolates had DPG, which is the first case in the genus Salicibibacter. The genomic G + C content of strains NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic analyses, strains NKC5-3T (= KACC 22040T = DSM 111417T) and NKC21-4T (= KACC 22041T = DSM 111418T) represent two novel species of the genus Salicibibacter, for which the names Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov. are proposed.
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Affiliation(s)
- Young Joon Oh
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon Yong Kim
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hak-Jong Choi
- Division of Research and Development, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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45
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Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench. Mar Drugs 2021; 19:md19050243. [PMID: 33923039 PMCID: PMC8146288 DOI: 10.3390/md19050243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/24/2022] Open
Abstract
A Micromonospora strain, isolate MT25T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1H-15N HSQC and 1H-15N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25T (NCIMB 15245T, TISTR 2834T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.
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46
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Hwang JH, Kim J, Kim JH, Mo S. Elizabethkingia argenteiflava sp. nov., isolated from the pod of soybean, Glycine max. Int J Syst Evol Microbiol 2021; 71. [PMID: 33835912 DOI: 10.1099/ijsem.0.004767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Soybean pods, separated and enclosed from the outside environment, are considered a suitable place to find new microbes. A Gram-stain-negative, aerobic bacterium, bacterial strain (YB22T) was isolated from the pod of Glycine max (soybean) collected from a rural area in Republic of Korea and characterized by using polyphasic taxonomy. Cells of the strain were rod-shaped (approximately 0.4-0.6 µm wide and 4.0-5.0 µm long), non-flagellated and formed silver-yellow colonies. Cells grew at 25-35 °C (optimum, 28-30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0-2.0% NaCl (optimum, 0 % NaCl). 16S rRNA gene sequencing showed that strain YB22T was phylogenetically closest to the genus Elizabethkingia, and showed highest similarities to Elizabethkingia occulta G4070T (96.7 %), Elizabethkingia meningoseptica ATCC 13253T (96.7 %), Elizabethkingia miricola DSM 14571T (96.6 %), Elizabethkingia bruuniana G0146T (96.5 %), Elizabethkingia ursingii G4122T (96.4 %) and Elizabethkingia anophelis R26T (96.2 %). Average amino acid identity values between strain YB22T and other taxa in the genus Elizabethkingia were all above the threshold range of genus determination. Average nucleotide identity and digital DNA-DNA hybridization values between strain YB22T and other phylogenetic relatives were all found to be below the threshold range for species determination. The respiratory quinone of strain YB22T was menaquinone 6 (MK-6) and the predominant cellular fatty acids were iso-C15 : 0 (47.8 %) and iso-C17 : 0 3-OH (18.5 %). The major polar lipids were phosphatidylethanolamine, four unidentified aminolipids and three unidentified polar lipids. The phylogenetic analysis and physiological and biochemical data showed that strain YB22T should represent a novel species in the genus Elizabethkingia, for which the name Elizabethkingia argenteiflava sp. nov. is proposed. The type strain for this novel species is YB22T (=KCCM 43263T=JCM 32097T).
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Affiliation(s)
- Jun-Hee Hwang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Jihyeon Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea
| | - Jae-Heon Kim
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - SangJoon Mo
- Medical Laser Research Center, Dankook University, Cheonan 31116, Republic of Korea
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47
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Shang DD, Lun HY, Zhu KL, Chen GJ, Du ZJ. Tenacibaculum pelagium sp. nov., isolated from marine sediment. Arch Microbiol 2021; 203:2229-2236. [PMID: 33629140 DOI: 10.1007/s00203-021-02208-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
A novel bright yellow pigmented, Gram-stain-negative, gliding, aerobic and rod-shaped marine bacterium, designated strain S7007T, was isolated from a marine sediment sample taken from Jingzi Wharf, Weihai, China. The bacterium was able to grow at 4-33 °C (optimum 28 °C), at pH 6.5-9.0 (optimum 7.0) and with 2.0-4.0% (w/v) NaCl (optimum 3.0%). According to the phylogenetic analysis based on the 16S rRNA gene sequences, strain S7007T was associated with the genus Tenacibaculum and showed highest similarity to Tenacibaculum adriaticum JCM 14633T (98.0%). The average nucleotide identity (ANI) scores of strain S7007T with T. adriaticum JCM 14633T and T. maritimum NBRC 110778T were 78.3% and 77.1%, respectively and the Genome-to-Genome Distance Calculator (dDDH) scores were 20.5% and 19.9%, respectively. The sole isoprenoid quinone was MK-6 and the major cellular fatty acids (> 10.0%) were iso-C15:0, iso-C15:0 3-OH, iso-C15: 1 G and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c). The major polar lipids of strain S7007T were phosphatidylethanolamine, phosphatidyldimethylethanolamine, one unidentified lipid and two unidentified aminolipids. The genomic DNA G + C content was 30.9 mol %. The combined phenotypic data and phylogenetic inference that strain S7007T should be classified as a novel species in the genus Tenacibaculum, for which the name Tenacibaculum pelagium sp. nov. is proposed. The type strain is S7007T (= MCCC 1H00428T = KCTC 72941T).
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Affiliation(s)
- Dan-Dan Shang
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - He-Yuan Lun
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Ke-Lei Zhu
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China. .,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, People's Republic of China.
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48
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Penna B, Silva MB, Soares AER, Vasconcelos ATR, Ramundo MS, Ferreira FA, Silva-Carvalho MC, de Sousa VS, Rabello RF, Bandeira PT, de Souza VS, Planet PJ, Vieira-da-Motta O, Botelho AMN, Figueiredo AMS. Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire. Sci Rep 2021; 11:4724. [PMID: 33633263 PMCID: PMC7907190 DOI: 10.1038/s41598-021-83993-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans-the main lineage found in Rio de Janeiro hospitals-to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.
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Affiliation(s)
- Bruno Penna
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Marcella B. Silva
- grid.412331.60000 0000 9087 6639Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - André E. R. Soares
- grid.452576.70000 0004 0602 9007Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Ana T. R. Vasconcelos
- grid.452576.70000 0004 0602 9007Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Mariana S. Ramundo
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabienne A. Ferreira
- grid.411237.20000 0001 2188 7235Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
| | - Maria C. Silva-Carvalho
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S. de Sousa
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata F. Rabello
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Paula T. Bandeira
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil ,grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S. de Souza
- grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paul J. Planet
- grid.25879.310000 0004 1936 8972Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Olney Vieira-da-Motta
- grid.412331.60000 0000 9087 6639Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Ana M. N. Botelho
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil ,grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Agnes M. S. Figueiredo
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Dos Santos Ferreira N, Hayashi Sant' Anna F, Massena Reis V, Ambrosini A, Gazolla Volpiano C, Rothballer M, Schwab S, Baura VA, Balsanelli E, Pedrosa FDO, Pereira Passaglia LM, Maltempi de Souza E, Hartmann A, Cassan F, Zilli JE. Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov. Int J Syst Evol Microbiol 2021; 70:6203-6212. [PMID: 33064068 DOI: 10.1099/ijsem.0.004517] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Azospirillum sp. strain Sp245T, originally identified as belonging to Azospirillum brasilense, is recognized as a plant-growth-promoting rhizobacterium due to its ability to fix atmospheric nitrogen and to produce plant-beneficial compounds. Azospirillum sp. Sp245T and other related strains were isolated from the root surfaces of different plants in Brazil. Cells are Gram-negative, curved or slightly curved rods, and motile with polar and lateral flagella. Their growth temperature varies between 20 to 38 °C and their carbon source utilization is similar to other Azospirillum species. A preliminary 16S rRNA sequence analysis showed that the new species is closely related to A. brasilense Sp7T and A. formosense CC-Nfb-7T. Housekeeping genes revealed that Azospirillum sp. Sp245T, BR 12001 and Vi22 form a separate cluster from strain A. formosense CC-Nfb-7T, and a group of strains closely related to A. brasilense Sp7T. Overall genome relatedness index (OGRI) analyses estimated based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between Azospirillum sp. Sp245T and its close relatives to other Azospirillum species type strains, such as A. brasilense Sp7T and A. formosense CC-Nfb-7T , revealed values lower than the limit of species circumscription. Moreover, core-proteome phylogeny including 1079 common shared proteins showed the independent clusterization of A. brasilense Sp7T, A. formosense CC-Nfb-7T and Azospirillum sp. Sp245T, a finding that was corroborated by the genome clustering of OGRI values and housekeeping phylogenies. The DNA G+C content of the cluster of Sp245T was 68.4-68.6 %. Based on the phylogenetic, genomic, phenotypical and physiological analysis, we propose that strain Sp245T together with the strains Vi22 and BR12001 represent a novel species of the genus Azospirillum, for which the name Azospirillum baldaniorum sp. nov. is proposed. The type strain is Sp245T (=BR 11005T=IBPPM 219T) (GCF_007827915.1, GCF_000237365.1, and GCF_003119195.2).
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Affiliation(s)
- Natalia Dos Santos Ferreira
- Programa de Pós-Graduação em Agronomia-Ciência do Solo, Universidade Federal Rural do Rio de Janeiro, BR 465 Km 7, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Fernando Hayashi Sant' Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Camila Gazolla Volpiano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum Muenchen, Ingolstaedter Landstr. 185764 Neuherberg, Germany
| | - Stefan Schwab
- Embrapa Agrobiologia, BR 465 Km 7, 23891-000, Seropédica, Rio de Janeiro, Brazil
| | - Valter Antonio Baura
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação de Nitrogênio, UFPR, Curitiba, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação de Nitrogênio, UFPR, Curitiba, Brazil
| | - Fabio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação de Nitrogênio, UFPR, Curitiba, Brazil
| | | | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação de Nitrogênio, UFPR, Curitiba, Brazil
| | - Anton Hartmann
- Faculty of Biology, Microbe-Host-Interactions, Ludwig-Maximilian-University Muenchen, 82152 Planegg/Martinsried, Germany
| | - Fabricio Cassan
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-microorganismo. Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), FCEFQyN. Universidad Nacional de Río Cuarto., Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
| | - Jerri Edson Zilli
- Embrapa Agrobiologia, BR 465 Km 7, 23891-000, Seropédica, Rio de Janeiro, Brazil
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Ghielmetti G, Rosato G, Trovato A, Friedel U, Kirchgaessner C, Perroulaz C, Pendl W, Schulthess B, Bloemberg GV, Keller PM, Stephan R, Tortoli E. Mycobacterium helveticum sp. nov., a novel slowly growing mycobacterial species associated with granulomatous lesions in adult swine. Int J Syst Evol Microbiol 2020; 71. [PMID: 33355527 PMCID: PMC7968739 DOI: 10.1099/ijsem.0.004615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The occurrence of nontuberculous mycobacteria in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. Mycobacteriosis in pigs is usually associated with members of the Mycobacterium avium complex and, in particular, with ‘Mycobacterium avium subsp. hominissuis’. Here we describe a novel slow-growing mycobacterial species isolated from lymph nodes obtained from two sows housed in different Swiss farms. The animals presented chronic inappetence and mild diarrhoea. Gross pathology revealed focal caseous lymphadenopathy of the mesenteric lymph nodes. Complete genome sequencing of the two isolates from the two sows was performed. The genomes comprised 5.76 Mb and an average nucleotide identity score of 99.97 %. Whole genome sequence, mycolic acid and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the two isolates were not related to any previously described Mycobacterium species. The closest related species was Mycobacterium parmense, a slow-growing scotochromogenic mycobacterium first isolated from a cervical lymph node of a 3-year-old child. The name proposed for the new species is Mycobacterium helveticum sp. nov. and 16-83T (=DSM 109965T= LMG 2019-02457T) is the type strain.
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Affiliation(s)
- Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Giovanni Ghielmetti,
| | - Giuliana Rosato
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Ute Friedel
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Constanze Kirchgaessner
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Carmen Perroulaz
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Wolfgang Pendl
- Department for Farm Animals, Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Bettina Schulthess
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Guido V. Bloemberg
- Institute for Food Safety and Hygiene, Swiss National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Peter M. Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
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