Pedobacter pituitosus sp. nov., isolated from a waterfall

Chun, Jeesun; Kang, Ji; Jahng, Kwang Yeop

doi:10.1099/ijs.0.065235-0

Cited by 11 publications

(3 citation statements)

References 14 publications

(9 reference statements)

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“…The genus Pedobacter was first described by Steyn et al ( 1998 ) to include heparinase-producing, obligate aerobic, Gram-negative rods discovered in soils and activated sludge. However, members of this genus have since been found in a wide array of environments, to include: freshwater lake sediment (An et al, 2009 ) and natural (Chun et al, 2014 ) and man-made water sources (Joung et al, 2010 ). The capabilities of most Pedobacter sp.…”

Section: Discussionmentioning

confidence: 99%

Characterization of shed medicinal leech mucus reveals a diverse microbiota

et al. 2015

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Microbial transmission through mucosal-mediated mechanisms is widespread throughout the animal kingdom. One example of this occurs with Hirudo verbana, the medicinal leech, where host attraction to shed conspecific mucus facilitates horizontal transmission of a predominant gut symbiont, the Gammaproteobacterium Aeromonas veronii. However, whether this mucus may harbor other bacteria has not been examined. Here, we characterize the microbiota of shed leech mucus through Illumina deep sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Additionally, Restriction Fragment Length Polymorphism (RFLP) typing with subsequent Sanger Sequencing of a 16S rRNA gene clone library provided qualitative confirmation of the microbial composition. Phylogenetic analyses of full-length 16S rRNA sequences were performed to examine microbial taxonomic distribution. Analyses using both technologies indicate the dominance of the Bacteroidetes and Proteobacteria phyla within the mucus microbiota. We determined the presence of other previously described leech symbionts, in addition to a number of putative novel leech-associated bacteria. A second predominant gut symbiont, the Rikenella-like bacteria, was also identified within mucus and exhibited similar population dynamics to A. veronii, suggesting persistence in syntrophy beyond the gut. Interestingly, the most abundant bacterial genus belonged to Pedobacter, which includes members capable of producing heparinase, an enzyme that degrades the anticoagulant, heparin. Additionally, bacteria associated with denitrification and sulfate cycling were observed, indicating an abundance of these anions within mucus, likely originating from the leech excretory system. A diverse microbiota harbored within shed mucus has significant potential implications for the evolution of microbiomes, including opportunities for gene transfer and utility in host capture of a diverse group of symbionts.

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Section: Discussionmentioning

confidence: 99%

Characterization of shed medicinal leech mucus reveals a diverse microbiota

et al. 2015

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“…Mostly Pedobacter species have been reported from soils (Yoon et al 2007;Luo et al 2010;Zhou et al 2012;Oh et al 2013). Members of this genus are ubiquitous in nature and some species have been reported from various environments such as a waterfall (Chung et al 2014), Hina Singh and Juan Du have contributed equally to this work.…”

Section: Introductionmentioning

confidence: 99%

Pedobacter lotistagni sp. nov. isolated from lotus pond water

Singh

Ngo

et al. 2015

Antonie van Leeuwenhoek

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A light-yellow coloured, Gram-stain negative, rod-shaped, aerobic, non-motile bacterium, designated THG-DN6.8(T), was isolated from a lotus pond near Donghaksa temple in Daejeon, South Korea. The strain was found to grow well on nutrient agar, optimally at pH 6.0-7.5, at temperature 25-28 °C and in the presence of 0.5 % NaCl. Based on 16S rRNA gene sequence analysis, strain THG-DN6.8(T) was found to share the highest sequence similarity with Pedobacter koreensis KCTC 12536(T), followed by Pedobacter glacialis CCTCC AB 2012941(T), Pedobacter kyungheensis KACC 16221(T), Pedobacter caeni LMG 22862(T), Pedobacter insulae KCTC 12820(T) and Pedobacter boryungensis KCTC 23344 (T). The DNA G+C content was determined to be 36.8 mol%. In DNA-DNA hybridization tests, the DNA relatedness between strain THG-DN6.8(T) and its closest phylogenetic neighbour P. koreensis was found to be below 10 %. The predominant isoprenoid quinone was identified as menaquinone MK-7 and the major polar lipid as phosphatidylethanolamine. The major fatty acids of strain THG-DN6.8(T) were identified as iso-C15:0, C16:0, C18:0 and C16:1 ω6c and/or C16:1 ω7c (summed feature 3). On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain THG-DN6.8(T) is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter lotistagni sp. nov. is proposed. The type strain is THG-DN6.8(T) (= KCTC 42229(T) = JCM 30354(T)).

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“…The complete genomes of Pedobacter deposited in the NCBI databases exhibit various genome sizes from 3.9 Mb (e.g., P. aquae CJ43 T ) to 6.3 Mb (e.g., P. roseus KACC 11594 T ) among the type strains. The habitats of the genus Pedobacter are widely distributed in various environments such as pine grove, forest soil, arctic soil, leaves, fragmentary rock, waterfalls, wood falls, and stream sediment [4–11]. In this study, we described a novel bacterial species, designated as strain ELA7 T from the faeces of eland ( Taurotragus oryx ) at Seoul Grand Park, a zoo in the Republic of Korea.…”

Section: Introductionmentioning

confidence: 99%

Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx

Park,

Min,

Kim

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Strain ELA7T, a novel Gram-negative, non-motile bacterium with a white pigment and rod-shaped morphology, was isolated from the faeces of an eland at Seoul Grand Park, a zoo in the Republic of Korea. The novel bacterial strain grew optimally in R2A medium under the following conditions: 0 % (w/v) NaCl, pH 8.0, and 34 °C. Based on phylogenetic analyses using 16S rRNA gene sequencing, strain ELA7T was found to have the closest relatedness to Pedobacter ginsengisoli Gsoil 104T (97.8 %), P. frigoris RP-3-15T (97.2 %), P. humi THG S15-2T (97.0 %), P. seoulensis THG-G12T (97.0 %), and P. foliorum LMG 31463T (96.9 %). The genome size and genomic DNA G+C content of strain ELA7T were 3.63 Mbp and 46.5 %, respectively. A whole genome-level comparison of strain ELA7T with P. ginsengisoli Gsoil 104T, P. frigoris RP-3-15T, P. africanus DSM 12126T, and P. psychroterrae RP-1-14T revealed average nucleotide identity values of 72.0, 71.8, 71.9, and 71.6 %, respectively. The major fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and MK-7 was the predominant respiratory quinone. The major polar lipids of strain ELA7T were phosphatidylethanolamine, sphingolipid, unidentified aminolipid, unidentified phosphoglycolipid, unidentified glycolipid, and eight unidentified lipids. Considering our chemotaxonomic, genotypic, and phenotypic findings, strain ELA7T (=KACC 23137T=JCM 36003T) is identified as representing a novel species within the genus Pedobacter, for which the name Pedobacter faecalis sp. nov. is proposed.

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Pedobacter pituitosus sp. nov., isolated from a waterfall

Cited by 11 publications

References 14 publications

Characterization of shed medicinal leech mucus reveals a diverse microbiota

Characterization of shed medicinal leech mucus reveals a diverse microbiota

Pedobacter lotistagni sp. nov. isolated from lotus pond water

Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx

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