1
|
de la Haba RR, Arahal DR, Sánchez-Porro C, Chuvochina M, Wittouck S, Hugenholtz P, Ventosa A. A long-awaited taxogenomic investigation of the family Halomonadaceae. Front Microbiol 2023; 14:1293707. [PMID: 38045027 PMCID: PMC10690426 DOI: 10.3389/fmicb.2023.1293707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 12/05/2023] Open
Abstract
The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.
Collapse
Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - David R. Arahal
- Departament of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| |
Collapse
|
2
|
Saeed A, Yasmin A, Baig M, Khan K, Heyat MBB, Akhtar F, Batool Z, Kazmi A, Wahab A, Shahid M, Ahmed MA, Abbas S, Muaad AY, Shahzad A, Ahmad I. Isolation and Characterization of Lactobacillus crispatus, Lactococcus lactis, and Carnobacterium divergens as Potential Probiotic Bacteria from Fermented Black and Green Olives ( Olea europaea): An Exploratory Study. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8726320. [PMID: 37152587 PMCID: PMC10156456 DOI: 10.1155/2023/8726320] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/02/2023] [Accepted: 02/16/2023] [Indexed: 05/09/2023]
Abstract
Background Table olives are becoming well recognized as a source of probiotic bacteria that might be used to create a health-promoting fermented food product by traditional procedures based on the activities of indigenous microbial consortia present in local environments. Methodology. In the present study, the characterization of probiotic bacteria isolated from mince, chunks, and brine of fermented green and black olives (Olea europaea) was done based on morphological, biochemical, and physiological characteristics. Results Bacterial isolates demonstrated excellent survival abilities at 25, 37, and 45°C and at a variable range of pH. However, the optimum temperature is 37 and the optimum pH is 7 for all three isolates. An antimicrobial susceptibility pattern was found among these isolates through the disc diffusion method. Most of the isolates were susceptible to streptomycin, imipenem, and chloramphenicol, whereas, amoxicillin showed resistance to these isolates, and variable results were recorded for the rest of the antibiotics tested. The growth of the isolates was optimum with the supplementation of 3% NaCl and 0.3% bile salt. The isolated bacteria were able to ferment skimmed milk into yogurt, hence making it capable of producing organic acid. Conclusion Isolates of Lactobacillus crispatus MB417, Lactococcus lactis MB418 from black olives, and Carnobacterium divergens MB421 from green olives were characterized as potential candidates for use as starter cultures to induce fermentation of other probiotic food products.
Collapse
Affiliation(s)
- Ayesha Saeed
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University Rawalpindi, Pakistan
| | - Azra Yasmin
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University Rawalpindi, Pakistan
| | - Mehreen Baig
- Surgical Unit II, Foundation University, Islamabad, Pakistan
| | - Khalid Khan
- Foot and Mouth Disease Vaccine Research Centre, Veterinary Research Institute (VRI), Peshawar, Pakistan
| | - Md Belal Bin Heyat
- IOT Research Centre, College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Centre for VLSI and Embedded System Technologies, International Institute of Information Technology, Hyderabad, Telangana 500032, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Faijan Akhtar
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Zahra Batool
- Institute of Innovative Development of Food Industry, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Abeer Kazmi
- Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences (UCAS), Wuhan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Abdul Wahab
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Muhammad Shahid
- Brucellosis Section, Veterinary Research Institute (VRI), Peshawar, Pakistan
| | | | - Sidra Abbas
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University Rawalpindi, Pakistan
| | | | - Amir Shahzad
- Nishtar Medical University, Multan, Punjab, Pakistan
| | - Imtiaz Ahmad
- Medical Officer, Regional Health Centre (RHC), Qadirabad, Tehsil Kot Chutta, District Dera Ghazi Khan, Punjab, Pakistan
| |
Collapse
|
3
|
Woods DF, Kozak IM, O'Gara F. Genome analysis and phenotypic characterization of Halomonas hibernica isolated from a traditional food process with novel quorum quenching and catalase activities. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36099016 DOI: 10.1099/mic.0.001238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Traditional food processes can utilize bacteria to promote positive organoleptic qualities and increase shelf life. Wiltshire curing has a vital bacterial component that has not been fully investigated from a microbial perspective. During the investigation of a Wiltshire brine, a culturable novel bacterium of the genus Halomonas was identified by 16S rRNA gene (MN822133) sequencing and analysis. The isolate was confirmed as representing a novel species (Halomonas hibernica B1.N12) using a housekeeping (HK) gene phylogenetic tree reconstruction with the selected genes 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA. The genome of the new isolate was sequenced and annotated and comparative genome analysis was conducted. Functional analysis revealed that the isolate has a unique phenotypic signature including high salt tolerance, a wide temperature growth range and substrate metabolism. Phenotypic and biochemical profiling demonstrated that H. hibernica B1.N12 possesses strong catalase activity which is an important feature for an industrial food processing bacterium, as it can promote an increased product shelf life and improve organoleptic qualities. Moreover, H. hibernica exhibits biocontrol properties based on its quorum quenching capabilities. Our work on this novel isolate advances knowledge on potential mechanistic interplays operating in complex microbial communities that mediate traditional food processes.
Collapse
Affiliation(s)
- David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Iwona M Kozak
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| |
Collapse
|
4
|
Yin YL, Li FL, Wang L. Halomonas salinarum sp. nov., a moderately halophilic bacterium isolated from saline soil in Yingkou, China. Arch Microbiol 2022; 204:466. [PMID: 35802152 PMCID: PMC9266089 DOI: 10.1007/s00203-022-03032-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 11/19/2022]
Abstract
Strain G5-11T, a Gram-negative, moderately halotolerant, facultatively aerobic, motile bacterium was isolated from saline soil collected from Yingkou, Liaoning, China. The cells of strain G5-11T grew in the presence of 3–15% (w/v) NaCl (optimum 5%), at between 4 and 35 °C (optimum 30 °C), and at a pH of 6.0–9.0 (optimum 8.0). The major respiratory quinone was Q-9 and the dominant cellular fatty acids were summed feature 8 (C18:1ω7c/C18:1ω6c), C16:0, and summed feature 3 (C16:1ω7c/C16:1ω6c). The major components of the polar lipid profile were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified aminolipid. The G + C content of the strain G5-11T genome was 61.0 mol%. The isolated strain G5-11T showed the highest 16S rRNA gene similarity to Halomonas niordiana LMG 31227T and Halomonas taeanensis DSM 16463T, both reaching 98.3%, followed by Halomonas pacifica NBRC 102220T. The results from phenotypic, chemotaxonomic, and phylogenetic analyses showed that strain G5-11T represented a novel species of the genus Halomonas, for which the name Halomonas salinarum sp. nov. was proposed. The type strain of Halomonas salinarum is G5-11T (= CGMCC 1.12051T = LMG 31677T).
Collapse
Affiliation(s)
- Ya-Lin Yin
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Fang-Ling Li
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lei Wang
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
| |
Collapse
|
5
|
Wang F, Wan JJ, Zhang XY, Xin Y, Sun ML, Wang P, Zhang WP, Tian JW, Zhang YZ, Li CY, Fu HH. Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, facultative anaerobic, non-flagellated, rod-shaped bacterial strains, designated MT13T and MT32, were isolated from sediment samples collected from the Mariana Trench at a depth of 8300 m. The two strains grew at −2–30 °C (optimum, 25 °C), at pH 5.5–10.0 (optimum, pH 7.5–8.0) and with 0–15 % (w/v) NaCl (optimum, 3–6 %). They did not reduce nitrate to nitrite nor hydrolyse Tweens 40 and 80, aesculin, casein, starch and DNA. The genomic G+C contents of draft genomes of strain MT13T and MT32 were 52.2 and 54.1 m ol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains MT13T and MT32 were affiliated with the genus
Halomonas
, with the highest similarity to the type strain of
Halomonas olivaria
. The values of average nucleotide identity and in silico DNA–DNA hybridization between strain MT13T and MT32, and between strain MT13T and five closely related type strains of
Halomonas
species indicated that strains MT13T and MT32 belonged to the same species, but represented a novel species in the genus of
Halomonas
. The major cellular fatty acids of strains MT13T and MT32 were C16 : 0, summed feature 3(C16 : 1
ω7c/ω6c) and summed feature 8 (C18 : 1
ω7c/ω6c). Major polar lipids of strains MT13T and MT32 included phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Ubiquinone-9 was the predominant respiratory quinone. Based on data from the present polyphasic study, strains MT13T and MT32 represent a novel species of the genus
Halomonas
, for which the name Halomonas profundi sp. nov. is proposed. The type strain is MT13T (=MCCC 1K06389T=KCTC 82923T).
Collapse
Affiliation(s)
- Fan Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Jin-Jian Wan
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Yu Xin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and Institute for Advanced Ocean Study, Ocean University of China, Qingdao, Shandong, PR China
| | - Mei-Ling Sun
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Wei-Peng Zhang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Ji-Wei Tian
- MOE Key Laboratory of Physical Oceanography and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, PR China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Chun-Yang Li
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Hui-Hui Fu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
| |
Collapse
|
6
|
Gago JF, Viver T, Urdiain M, Pastor S, Kämpfer P, Ferreira E, Rossello-Mora R. Description of three new Alteromonas species Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. isolated from marine environments, and proposal for reclassification of the genus Salinimonas as Alteromonas. Syst Appl Microbiol 2021; 44:126226. [PMID: 34171620 DOI: 10.1016/j.syapm.2021.126226] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 11/26/2022]
Abstract
In the course of a bioprospective study of marine prokaryotes for cosmetic purposes, four strains, MD_567T, MD_652T, MD_674 and PS_109T, were isolated that 16S rRNA gene affiliation indicated could represent three new species within the family Alteromonadaceae. A thorough phylogenetic, genomic and phenotypic taxonomic study confirmed that the isolates could be classified as three new taxa for which we propose the names Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. In addition, the consistent monophyletic nature of the members of the genera Alteromonas and Salinimonas showed that both taxa should be unified, and therefore we also propose the reclassification of the genus Salinimonas within Alteromonas, as well as new combinations for the species of the former. As the specific epithets profundi and sediminis are already used for Alteromonas species, we created the nomina nova "Alteromonas alteriprofundi" nom. nov. and Alteromonas alterisediminis nom. nov. to accommodate the new names for "Salinimonas profundi" and Salinimonas sediminis. Whole genome comparisons also allowed us to detect the unexpected codification of aromatic hydrocarbon biodegradative compounds, such as benzoate and catechol, whose activity was then demonstrated phenotypically. Finally, the high genomic identity between the type strains of Alteromonas stellipolaris and Alteromonas addita indicated that the latter is a junior heterotypic synonym of Alteromonas stellipolaris.
Collapse
Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | | | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| |
Collapse
|
7
|
Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2020; 70:2960-2966. [PMID: 32471528 DOI: 10.1099/ijsem.0.004156] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|