Journal of Microbiology

Research Support, Non-U.S. Gov'ts

Analysis of Bacterial Diversity in Sponges Collected from Chuuk and Kosrae Islands in Micronesia: In-Hye Jeong , Kyoung-Ho Kim , Hyi-Seung Lee , Jin-Sook Park; J. Microbiol. 2014;52(1):20-26. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3619-x

61 View
0 Download
3 Crossref

The bacteria resident in sponges collected from Chuuk Lagoon and Kosrae Island of Micronesia were investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. These sponges were clustered into 5 groups based on their bacterial composition. Diversity indexes and cumulative rank abundance curves showed the different compositions of bacterial communities in the various groups of sponges. Reads related to the phylum Chloroflexi were observed predominantly (9.7–68.2%) in 9 sponges of 3 groups and unobserved in the other 2 groups. The Chloroflexi-containing group had similar bacterial patterns at the phylum and lower taxonomic levels, for example, significant proportions of Acidobacteria, Gemmatimonadetes, SBR1093, and PAUC34f were observed in most members of this group. The three groups in the Chloroflexi- containing group, however, showed some minor differences in the composition and diversity. The other two groups contained high proportions of Proteobacteria (>87%) or Bacteroidetes (>61%) and different composition and diversity compared to the Chloroflexi-containing group and each other. Four pairs of specimens with the same species showed similar bacterial profiles, but, the bacteria in sponges were highly specific at the individual level.

Citations

Citations to this article as recorded by

Identification of marine sponge-associated bacteria of the Saint Martin's island of the Bay of Bengal emphasizing on the prevention of motile Aeromonas septicemia in Labeo rohita
Sulav Indra Paul, Md. Mahbubur Rahman, Mohammad Abdus Salam, Md. Arifur Rahman Khan, Md. Tofazzal Islam
Aquaculture.2021; 545: 737156. CrossRef
First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing
Akram Najafi, Maryam Moradinasab, Iraj Nabipour
Frontiers in Microbiology.2018;[Epub] CrossRef
Acidobacteriaappear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid
Aileen O’Connor-Sánchez, Adán J Rivera-Domínguez, César De los Santos-Briones, Lluvia K López-Aguiar, Yuri J Peña-Ramírez, Alejandra Prieto-Davo
Biological Research.2014;[Epub] CrossRef

Analysis of Bacterial Diversity in Sponges Collected off Chujado, an Island in Korea, Using Barcoded 454 Pyrosequencing: Analysis of a Distinctive Sponge Group Containing Chloroflexi: In-Hye Jeong , Kyoung-Ho Kim , Jin-Sook Park; J. Microbiol. 2013;51(5):570-577. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3426-9

62 View
0 Download
12 Crossref

Abstract

The bacterial diversity of 14 sponges belonging to 5 different orders that were collected around Chuja Island, Korea was investigated using barcoded 454 pyrosequencing. The sponges contained many unidentified bacterial groups (e.g. more than half of the taxa at the family level) that were known only in environmental sequences and obtained from culture-independent methods. Five of the sponges were clustered into one notable group (CF group), which was distinguished from the other sponges in accordance with bacterial composition (the other sponges may be separated into more groups but clustering is not clear). The CF group contained high amounts of Chloroflexi (25.0–47.7%) and moderate amounts of Gemmatimonadetes (2.3–7.0%), AncK6 (0.6–2.2%), PAUC34f (0.8–6.0%), Acidobacteria (3.7–9.6%), and SBR1093 (1.8–5.6%) exclusively or almost exclusively to this group. Sponges in the CF group also showed higher diversity (e.g. Shannon index) than the other sponges and contained group-specific taxonomic lineages (e.g. class or family level) from group-specific phyla and even from the Proteobacteria and Actinobacteria, which were detected in all sponges at the phylum level. The CF group may be one of the most distinctive groups in sponges in terms of bacterial diversity.

Citations

Citations to this article as recorded by

The effect of environmental and anthropogenic factors on the microbiome of the sponge, Halichondria panicea, at three coastal sites with different bathing water quality in North east England
Sakinah Al-Haddad, Gary S. Caldwell, Anthony S. Clare
Aquatic Sciences.2025;[Epub] CrossRef
Diversity and functional roles of the symbiotic microbiome associated to marine sponges off Karah Island, Terengganu, Malaysia
Yuki Hayami, Logajothiswaran Ambalavanan, Sandra Catherine Zainathan, Muhd Danish-Daniel, Noor Emilia Sharifah, Shumpei Iehata
Regional Studies in Marine Science.2023; 62: 102967. CrossRef
Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea, Saudi Arabia
Fehmida Bibi, Sana Akhtar Alvi, Abdulmohsin Al-Sofyani, Muhammad Imran Naseer, Muhammad Yasir, Esam Ibraheem Azhar
Saudi Journal of Biological Sciences.2020; 27(1): 67. CrossRef
First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing
Akram Najafi, Maryam Moradinasab, Iraj Nabipour
Frontiers in Microbiology.2018;[Epub] CrossRef
Prokaryote composition and predicted metagenomic content of two Cinachyrella Morphospecies and water from West Papuan Marine Lakes
Daniel F R Cleary, Ana R M Polónia, Nicole J de Voogd
FEMS Microbiology Ecology.2018;[Epub] CrossRef
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico “Dead Zone”
J. Cameron Thrash, Kiley W. Seitz, Brett J. Baker, Ben Temperton, Lauren E. Gillies, Nancy N. Rabalais, Bernard Henrissat, Olivia U. Mason, Mary Ann Moran
mBio.2017;[Epub] CrossRef
Intestinal microecology associated with fluoride resistance capability of the silkworm (Bombyx mori L.)
Guan-Nan Li, Xue-Juan Xia, Wen-Chao Tang, Yong Zhu
Applied Microbiology and Biotechnology.2016; 100(15): 6715. CrossRef
In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity
Georg Steinert, Michael W. Taylor, Peter Deines, Rachel L. Simister, Nicole J. de Voogd, Michael Hoggard, Peter J. Schupp
PeerJ.2016; 4: e1936. CrossRef
Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash
Jae Ho Joa, Hang Yeon Weon, Hae Nam Hyun, Young Chull Jeun, Sang Wook Koh
Journal of Microbiology.2014; 52(12): 995. CrossRef
Two distinct microbial communities revealed in the sponge Cinachyrella
Marie L. Cuvelier, Emily Blake, Rebecca Mulheron, Peter J. McCarthy, Patricia Blackwelder, Rebecca L. Vega Thurber, Jose V. Lopez
Frontiers in Microbiology.2014;[Epub] CrossRef
Analysis of bacterial diversity in sponges collected from chuuk and kosrae islands in micronesia
In-Hye Jeong, Kyoung-Ho Kim, Hyi-Seung Lee, Jin-Sook Park
Journal of Microbiology.2014; 52(1): 20. CrossRef
Bacterial Diversity of the South Pacific Sponge, Dactylospongia metachromia Based on DGGE Fingerprinting
In-Hye Jeong, Jin-Sook Park
The Korean Journal of Microbiology.2013; 49(4): 377. CrossRef

PyroTrimmer: a Software with GUI for Pre-Processing 454 Amplicon Sequences: Jeongsu Oh , Byung Kwon Kim , Wan-Sup Cho , Soon Gyu Hong , Kyung Mo Kim; J. Microbiol. 2012;50(5):766-769. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2494-6

42 View
0 Download
21 Scopus

Abstract: The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct lowquality sequences. We have developed a program called Pyro-Trimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.

SP0454, A Putative Threonine Dehydratase, Is Required For Pneumococcal Virulence In Mice: WenJuan Yan , Hong Wang , WenChun Xu , KaiFeng Wu , Run Yao , XiuYu Xu , Jie Dong , YanQing Zhang , Wen Zhong , XueMei Zhang; J. Microbiol. 2012;50(3):511-517. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2014-8

34 View
0 Download
6 Scopus

Abstract: Increasing pressure in antibiotic resistance and the requirement for the design of new vaccines are the objectives of clarifying the putative virulence factors in pneumococcal infection. In this study, the putative threonine dehydratase sp0454 was inactivated by erythromycin-resistance cassette replacement in Streptococcus pneumoniae CMCC 31203 strain. The sp0454 mutant was tested for cell growth, adherence, colonization, and virulence in a murine model. The Δsp0454 mutant showed decreased ability for colonization and impaired ability to adhere to A549 cells. However, the SP0454 polypeptide or its antiserum did not affect pneumococcal CMCC 31203 adhesion to A549 cells. The sp0454 deletion mutant was less virulent in a murine intranasal infection model. Real-time RT-PCR analysis revealed significant decrease of the pneumococcal surface antigen A expression in the sp0454 mutant. These results suggest that SP0454 contributes to virulence and colonization, which could be explained in part by modulating the expression of other virulence factors, such as psaA in pneumococcal infection.

Comparative Approach to Capture Bacterial Diversity of Coastal Waters: Hyunsoo Na , Ok-Sun Kim , Seok-Hwan Yoon , Yunmin Kim , Jongsik Chun; J. Microbiol. 2011;49(5):729-740. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1205-z

44 View
0 Download
17 Scopus

Abstract: Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1% of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.

First
Prev
Page of 1
Next
Last

Search