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Pascual J, Lepleux C, Methner A, Spröer C, Bunk B, Overmann J. Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37200211 DOI: 10.1099/ijsem.0.005895] [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: 05/20/2023] Open
Abstract
A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2T, was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2T was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2T was closely related to Arcobacter lekithochrous LFT 1.7T and Arcobacter caeni RW17-10T(95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2T was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2T represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2T as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2T (DSM 29169T=KCTC 52423T).
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Affiliation(s)
- Javier Pascual
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
- Present address: Darwin Bioprospecting Excellence S.L., Paterna, Spain
| | - Cendrella Lepleux
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Cathrin Spröer
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
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A Review on the Prevalence of Arcobacter in Aquatic Environments. WATER 2022. [DOI: 10.3390/w14081266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Arcobacter is an emerging pathogen that is associated with human and animal diseases. Since its first introduction in 1991, 33 Arcobacter species have been identified. Studies have reported that with the presence of Arcobacter in environmental water bodies, animals, and humans, a possibility of its transmission via water and food makes it a potential waterborne and foodborne pathogen. Therefore, this review article focuses on the general characteristics of Arcobacter, including its pathogenicity, antimicrobial resistance, methods of detection by cultivation and molecular techniques, and its presence in water, fecal samples, and animal products worldwide. These detection methods include conventional culture methods, and rapid and accurate Arcobacter identification at the species level, using quantitative polymerase chain reaction (qPCR) and multiplex PCR. Arcobacter has been identified worldwide from feces of various hosts, such as humans, cattle, pigs, sheep, horses, dogs, poultry, and swine, and also from meat, dairy products, carcasses, buccal cavity, and cloacal swabs. Furthermore, Arcobacter has been detected in groundwater, river water, wastewater (influent and effluent), canals, treated drinking water, spring water, and seawater. Hence, we propose that understanding the prevalence of Arcobacter in environmental water and fecal-source samples and its infection of humans and animals will contribute to a better strategy to control and prevent the survival and growth of the bacteria.
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Li S, Young T, Archer S, Lee K, Sharma S, Alfaro AC. Mapping the Green-Lipped Mussel (Perna canaliculus) Microbiome: A Multi-Tissue Analysis of Bacterial and Fungal Diversity. Curr Microbiol 2022; 79:76. [PMID: 35091849 PMCID: PMC8799583 DOI: 10.1007/s00284-021-02758-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/28/2021] [Indexed: 11/03/2022]
Abstract
Poor health and mortality events of the commercially important and endemic New Zealand green-lipped mussel (Perna canaliculus) pose a threat to its industry. Despite the known importance of microbiomes to animal health and environmental resilience, the host-associated microbiome is unexplored in this species. We conducted the first baseline characterization of bacteria and fungi within key host tissues (gills, haemolymph, digestive gland, and stomach) using high-throughput amplicon sequencing of 16S rRNA gene and ITS1 region for bacteria and fungi, respectively. Tissue types displayed distinctive bacterial profiles, consistent among individuals, that were dominated by phyla which reflect (1) a fluid exchange between the circulatory system (gills and haemolymph) and surrounding aqueous environment and (2) a highly diverse digestive system (digestive gland and stomach) microbiota. Gammaproteobacteria and Campylobacterota were mostly identified in the gill tissue and haemolymph, and were also found in high abundance in seawater. Digestive gland and stomach tissues were dominated by common gut bacterial phyla, such as Firmicutes, Cyanobacteria, Proteobacteria, and Bacteroidota, which reflects the selectivity of the digestive system and food-based influences. Other major notable taxa included the family Spirochaetaceae, and genera Endozoicomonas, Psychrilyobacter, Moritella and Poseidonibacter, which were highly variable among tissue types and samples. More than 50% of fungal amplicon sequence variants (ASVs) were unclassified beyond the phylum level, which reflects the lack of studies with marine fungi. However, the majority of those identified were assigned to the phylum Ascomycota. The findings from this work provide the first insight into healthy tissue microbiomes of P. canaliculus and is of central importance to understanding the effect of environmental changes on farmed mussels at the microbial level.
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Affiliation(s)
- Siming Li
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag, 92006, Auckland, 1142, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag, 92006, Auckland, 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag, 92006, Auckland, 1142, New Zealand
| | - Stephen Archer
- Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag, 92006, Auckland, 1142, New Zealand
| | - Kevin Lee
- Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag, 92006, Auckland, 1142, New Zealand
| | - Shaneel Sharma
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag, 92006, Auckland, 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, Faculty of Health and Environmental Sciences, School of Science, Auckland University of Technology, Private Bag, 92006, Auckland, 1142, New Zealand.
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On SLW, Miller WG, Biggs PJ, Cornelius AJ, Vandamme P. Aliarcobacter, Halarcobacter, Malaciobacter, Pseudarcobacter and Poseidonibacter are later synonyms of Arcobacter: transfer of Poseidonibacter parvus, Poseidonibacter antarcticus, ' Halarcobacter arenosus', and ' Aliarcobacter vitoriensis' to Arcobacter as Arcobacter parvus comb. nov., Arcobacter antarcticus comb. nov., Arcobacter arenosus comb. nov. and Arcobacter vitoriensis comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34825881 DOI: 10.1099/ijsem.0.005133] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper re-examines the taxonomic positions of recently described Poseidonibacter (P. parvum and P. antarcticus), Aliarcobacter ('Al. vitoriensis'), Halarcobacter ('H. arenosus') and Arcobacter (A. caeni, A. lacus) species, and other species proposed to represent novel genera highly related to the genus Arcobacter. Phylogenomic and several overall genome relatedness indices (OGRIs) were applied to a total of 118 representative genomes for this purpose. Phylogenomic analyses demonstrated the Arcobacter clade to be distinct from other Epsilonproteobacteria, clearly defined and containing closely related species. Aliarcobacter butzleri and Malaciobacter pacificus did not cluster with other members of these proposed genera, indicating incoherence of these genera. Every OGRI measure applied indicated a high level of relatedness among all Arcobacter clade species, including the recently described taxa studied here, and substantially lower between type species representatives for other Epsilonproteobacteria. Where published guidelines were available, OGRI values for Arcobacter clade species were either unsupportive of division into other genera or were at the lowest boundary range (for average amino acid identity). We propose that Aliarcobacter, Halarcobacter, Malaciobacter, Pseudarcobacter, Poseidonibacter and Arcobacter sensu stricto be considered members of a single genus, Arcobacter, and subsequently transfer P. parvum, P. antarcticus, 'Al. vitoriensis' and 'H. arenosus' to Arcobacter as Arcobacter parvum comb. nov., Arcobacter antarcticus comb. nov., Arcobacter vitoriensis comb. nov. and Arcobacter arenosus comb. nov.
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Affiliation(s)
- Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Springs Road, Lincoln, 7467 New Zealand
| | - William G Miller
- US Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Patrick J Biggs
- Bioinformatics and Statistics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Angela J Cornelius
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000, Ghent, Belgium
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Kim MJ, Baek MG, Shin SK, Yi H. Poseidonibacter parvus sp. nov., isolated from a squid. Int J Syst Evol Microbiol 2020; 71. [PMID: 33269998 DOI: 10.1099/ijsem.0.004590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, short rod-shaped, motile, brownish-coloured bacterium, termed strain LPB0137T, was isolated from a squid. Its cells could grow weakly on marine agar 2216 with 0.04 % 2,3,5-triphenyl tetrazolium chloride (TTC). Each cell of strain LPB0137T has a circular chromosome with a length of 2.87 Mb and 27.7 mol% DNA G+C content. The genome includes 2698 protein-coding genes and six rRNA operons. In 16S rRNA gene sequence trees, strain LPB0137T formed a robust monophyletic clade with Poseidonibacter antarcticus SM1702T with a sequence similarity of 98.3 %. However, the average nucleotide identity and in silico DNA-DNA hybridization values between the two type strains were low (83.9 and 28.1 %, respectively). The overall phenotypic and genomic features of strain LPB0137T supported its assignment to the genus Poseidonibacter. However, the relatively low gene and genome sequence similarity between this strain and other type strains of the genus Poseidonibacter and several enzymatic characteristics indicated the taxonomic novelty of the isolated strain as a new member of the genus Poseidonibacter. Therefore, based on the phylogenetic and phenotypic characteristics of LPB0137T, we proposed a novel species of the genus Poseidonibacter for it, with the name Poseidonibacter parvus sp. nov. The type strain of this new species is thus LPB0137T (=KACC 18888T=JCM 31548T).
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Affiliation(s)
- Min Ji Kim
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Min-Gyung Baek
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Su-Kyoung Shin
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea.,Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
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